renaming BioC XML files to show PMC ID as file name and to be able to distinguish between raw and annotated XML; add folder with JSON version of annotated BioC

LICENSE.md

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2023, Melanie Vollmar
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

annotated_BioC_JSON/PMC4854314_ann.json

@@ -0,0 +1 @@
+[{"sourceid":"4854314","sourcedb":"","project":"","target":"","text":"RNA protects a nucleoprotein complex against radiation damage Systematic analysis of radiation damage within a protein–RNA complex over a large dose range (1.3–25 MGy) reveals significant differential susceptibility of RNA and protein. A new method of difference electron-density quantification is presented. Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3–25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein–DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density. Introduction    With the wide use of high-flux third-generation synchrotron sources, radiation damage (RD) has once again become a dominant reason for the failure of structure determination using macromolecular crystallography (MX) in experiments conducted both at room temperature and under cryocooled conditions (100 K). Significant progress has been made in recent years in understanding the inevitable manifestations of X-ray-induced RD within protein crystals, and there is now a body of literature on possible strategies to mitigate the effects of RD (e.g. Zeldin, Brockhauser et al., 2013; Bourenkov \u0026 Popov, 2010). However, there is still no general consensus within the field on how to minimize RD during MX data collection, and debates on the dependence of RD progression on incident X-ray energy (Shimizu et al., 2007; Liebschner et al., 2015) and the efficacy of radical scavengers (Allan et al., 2013) have yet to be resolved. RD manifests in two forms. Global radiation damage is observed within reciprocal space as the overall decay of the summed intensity of reflections detected within the diffraction pattern as dose increases (Garman, 2010; Murray \u0026 Garman, 2002). Dose is defined as the absorbed energy per unit mass of crystal in grays (Gy; 1 Gy = 1 J kg−1), and is the metric against which damage progression should be monitored during MX data collection, as opposed to time. At 100 K, an experimental dose limit of 30 MGy has been recommended as an upper limit beyond which the biological information derived from any macromolecular crystal may be compromised (Owen et al., 2006).  Specific radiation damage (SRD) is observed in the real-space electron density, and has been detected at much lower doses than any observable decay in the intensity of reflections. Indeed, the C—Se bond in selenomethionine, the stability of which is key for the success of experimental phasing methods, can be cleaved at a dose as low as 2 MGy for a crystal maintained at 100 K (Holton, 2007). SRD has been well characterized in a large range of proteins, and is seen to follow a reproducible order: metallo-centre reduction, disulfide-bond cleavage, acidic residue decarboxylation and methionine methylthio cleavage (Ravelli \u0026 McSweeney, 2000; Burmeister, 2000; Weik et al., 2000; Yano et al., 2005). Furthermore, damage susceptibility within each residue type follows a preferential ordering influenced by a combination of local environment factors (solvent accessibility, conformational strain, proximity to active sites/high X-ray cross-section atoms; Holton, 2009). Deconvoluting the individual roles of these parameters has been surprisingly challenging, with factors such as solvent accessibility currently under active investigation (Weik et al., 2000; Fioravanti et al., 2007; Gerstel et al., 2015). There are a number of cases where SRD manifestations have compromised the biological information extracted from MX-determined structures at much lower doses than the recommended 30 MGy limit, leading to false structural interpretations of protein mechanisms. Active-site residues appear to be particularly susceptible, particularly for photosensitive proteins and in instances where chemical strain is an intrinsic feature of the reaction mechanism. For instance, structure determination of the purple membrane protein bacterio­rhodopsin required careful corrections for radiation-induced structural changes before the correct photosensitive intermediate states could be isolated (Matsui et al., 2002). The significant chemical strain required for catalysis within the active site of phosphoserine aminotransferase has been observed to diminish during X-ray exposure (Dubnovitsky et al., 2005). Since the majority of SRD studies to date have focused on proteins, much less is known about the effects of X-ray irradiation on the wider class of crystalline nucleoprotein complexes or how to correct for such radiation-induced structural changes. Understanding RD to such complexes is crucial, since DNA is rarely naked within a cell, instead dynamically interacting with proteins, facilitating replication, transcription, modification and DNA repair. As of early 2016, \u003e5400 nucleoprotein complex structures have been deposited within the PDB, with 91% solved by MX. It is essential to understand how these increasingly complex macromolecular structures are affected by the radiation used to solve them. Nucleoproteins also represent one of the main targets of radiotherapy, and an insight into the damage mechanisms induced by X-ray irradiation could inform innovative treatments. When a typical macromolecular crystal is irradiated with ionizing X-rays, each photoelectron produced via interactions with both the macromolecule (direct damage) and solvent (indirect damage) can induce cascades of up to 500 secondary low-energy electrons (LEEs) that are capable of inducing further ionizations. Investigations on sub-ionization-level LEEs (0–15 eV) interacting with both dried and aqueous oligonucleotides (Alizadeh \u0026 Sanche, 2014; Simons, 2006) concluded that resonant electron attachment to DNA bases and the sugar-phosphate backbone could lead to the preferential cleavage of strong (∼4 eV, 385 kJ mol−1) sugar-phosphate C—O covalent bonds within the DNA backbone and then base-sugar N1—C bonds, eventually leading to single-strand breakages (SSBs; Ptasińska \u0026 Sanche, 2007). Electrons have been shown to be mobile at 77 K by electron spin resonance spectroscopy studies (Symons, 1997; Jones et al., 1987), with rapid electron quantum tunnelling and positive hole migration along the protein backbone and through stacked DNA bases indicated as a dominant mechanism by which oxidative and reductive damage localizes at distances from initial ionization sites at 100 K (O’Neill et al., 2002). The investigation of naturally forming nucleoprotein complexes circumvents the inherent challenges in making controlled comparisons of damage mechanisms between protein and nucleic acids crystallized separately. Recently, for a well characterized bacterial protein–DNA complex (C.Esp1396I; PDB entry 3clc; resolution 2.8 Å; McGeehan et al., 2008) it was concluded that over a wide dose range (2.1–44.6 MGy) the protein was far more susceptible to SRD than the DNA within the crystal (Bury et al., 2015). Only at doses above 20 MGy were precursors of phosphodiester-bond cleavage observed within AT-rich regions of the 35-mer DNA. For crystalline complexes such as C.Esp1396I, whether the protein is intrinsically more susceptible to X-ray-induced damage or whether the protein scavenges electrons to protect the DNA remains unclear in the absence of a non-nucleic acid-bound protein control obtained under exactly the same crystallization and data-collection conditions. To monitor the effects of nucleic acid binding on protein damage susceptibility, a crystal containing two protein molecules per asymmetric unit, only one of which was bound to RNA, is reported here (Fig. 1 ▸). Using newly developed methodology, we present a controlled SRD investigation at 1.98 Å resolution using a large (∼91 kDa) crystalline protein–RNA complex: trp RNA-binding attenuation protein (TRAP) bound to a 53 bp RNA sequence (GAGUU)10GAG (PDB entry 1gtf; Hopcroft et al., 2002). TRAP consists of 11 identical subunits assembled into a ring with 11-fold rotational symmetry. It binds with high affinity (K d ≃ 1.0 nM) to RNA segments containing 11 GAG/UAG triplets separated by two or three spacer nucleotides (Elliott et al., 2001) to regulate the transcription of tryptophan biosynthetic genes in Bacillus subtilis (Antson et al., 1999). In this structure, the bases of the G1-A2-G3 nucleotides form direct hydrogen bonds to the protein, unlike the U4-U5 nucleotides, which appear to be more flexible. Ten successive 1.98 Å resolution MX data sets were collected from the same TRAP–RNA crystal to analyse X-ray-induced structural changes over a large dose range (d 1 = 1.3 MGy to d 10 = 25.0 MGy). To avoid the previous necessity for visual inspection of electron-density maps to detect SRD sites, a computational approach was designed to quantify the electron-density change for each refined atom with increasing dose, thus providing a rapid systematic method for SRD study on such large multimeric complexes. By employing the high 11-fold structural symmetry within each TRAP macromolecule, this approach permitted a thorough statistical quantification of the RD effects of RNA binding to TRAP. Materials and methods    RNA synthesis and protein preparation    As previously described (Hopcroft et al., 2002), the 53-base RNA (GAGUU)10GAG was synthesized by in vitro transcription with T7 RNA polymerase and gel-purified. TRAP from B. stearothermophilus was overexpressed in Escherichia coli and purified. Crystallization    TRAP–RNA crystals were prepared using a previously established hanging-drop crystallization protocol (Antson et al., 1999). By using a 2:1 molar ratio of TRAP to RNA, crystals successfully formed from the protein–RNA complex (∼15 mg ml−1) in a solution containing 70 mM potassium phosphate pH 7.8 and 10 mM l-tryptophan. The reservoir consisted of 0.2 M potassium glutamate, 50 mM triethanol­amine pH 8.0, 10 mM MgCl2, 8–11% monomethyl ether PEG 2000. In order to accelerate crystallization, a further gradient was induced by adding 0.4 M KCl to the reservoir after 1.5 µl protein solution had been mixed with an equal volume of the reservoir solution. Wedge-shaped crystals of approximate length 70 µm (longest dimension) grew within 3 d and were vitrified and stored in liquid nitrogen immediately after growth. The cryosolution consisted of 12% monomethyl ether PEG 2000, 30 mM triethanolamine pH 8.0, 6 mM l-tryptophan, 0.1 M potassium glutamate, 35 mM potassium phosphate pH 7.8, 5 mM MgCl2 with 25% 2-methyl-2,4-pentanediol (MPD) included as a cryoprotectant. X-ray data collection    Data were collected at 100 K from a wedge-shaped TRAP–RNA crystal of approximate dimensions 70 × 20 × 40 µm (see Supplementary Fig. S2) on beamline ID14-4 at the ESRF using an incident wavelength of 0.940 Å (13.2 keV) and an ADSC Q315R mosaic CCD detector at 304.5 mm from the crystal throughout the data collection. The beam size was slitted to 0.100 mm (vertical) × 0.160 mm (horizontal), with a uniformly distributed profile, such that the crystal was completely bathed within the beam throughout data collection. Ten successive (1.98 Å resolution) 180° data sets (with Δφ = 1°) were collected over the same angular range from a TRAP–RNA crystal at 28.9% beam transmission. The TRAP–RNA macromolecule crystallized in space group C2, with unit-cell parameters a = 140.9, b = 110.9, c = 137.8 Å, α = γ = 90, β = 137.8° (the values quoted are for the first data set; see Supplementary Table S1 for subsequent values). For the first nine data sets the attenuated flux was recorded to be ∼5 × 1011 photons s−1. A beam refill took place immediately before data set 10, requiring a flux-scale factor increase of 1.42 to be applied, based on the ratio of observed relative intensity I D/I 1 at data set 10 to that extrapolated from data set 9. Dose calculation     RADDOSE-3D (Zeldin, Gerstel et al., 2013) was used to calculate the absorbed dose distribution during each data set (see input file; Supplementary Figs. S1 and S2). The crystal composition was calculated from the deposited TRAP–RNA structure (PDB entry 1gtf; Hopcroft et al., 2002). Crystal absorption coefficients were calculated in RADDOSE-3D using the concentration (mmol l−1) of solvent heavy elements from the crystallization conditions. The beam-intensity profile was modelled as a uniform (‘top-hat’) distribution. The diffraction-weighted dose (DWD) values (Zeldin, Brock­hauser et al., 2013) are given in Supplementary Table S1. Data processing and model refinement    Each data set was integrated using iMosflm (Leslie \u0026 Powell, 2007) and was scaled using AIMLESS (Evans \u0026 Murshudov, 2013; Winn et al., 2011) using the same 5% R free set of test reflections for each data set. To phase the structure obtained from the first data set, molecular replacement was carried out with Phaser (McCoy et al., 2007), using an identical TRAP–RNA structure (PDB entry 1gtf; resolution 1.75 Å; Hopcroft et al., 2002) as a search model. The resulting TRAP–RNA structure (TR1) was refined using REFMAC5 (Murshudov et al., 2011), initially using rigid-body refinement, followed by repeated cycles of restrained, TLS and isotropic B-factor refinement, coupled with visual inspection in Coot (Emsley et al., 2010). TR1 was refined to 1.98 Å resolution, with a dimeric assembly of non-RNA-bound and RNA-bound TRAP rings within the asymmetric unit. Consistent with previous structures of the TRAP–RNA complex, the RNA sequence termini were not observed within the 2F o − F c map; the first spacer (U4) was then modelled at all 11 repeats around the TRAP ring and the second spacer (U5) was omitted from the final refined structure. For the later data sets, the observed structure-factor amplitudes from each separately scaled data set (output from AIMLESS) were combined with the phases of TR1 and the resulting higher-dose model was refined with phenix.refine (Adams et al., 2010) using only rigid-body and isotropic B-factor refinement. During this refinement, the TRAP–RNA complex and nonbound TRAP ring were treated as two separate rigid bodies within the asymmetric unit. Supplementary Table S1 shows the relevant summary statistics.  D loss metric calculation    The CCP4 program CAD was used to create a series of nine merged .mtz files combining observed structure-factor amplitudes for the first data set F obs(d 1) with each later data set F obs(d n) (for n = 2, …, 10). All later data sets were scaled against the initial low-dose data set in SCALEIT. For each data set an atom-tagged .map file was generated using the ATMMAP mode in SFALL (Winn et al., 2011). A full set of nine Fourier difference maps F obs(d n) − F obs(d 1) were calculated using FFT (Ten Eyck, 1973) over the full TRAP–RNA unit-cell dimensions, with the same grid-sampling dimensions as the atom-tagged .map file. All maps were cropped to the TRAP asymmetric unit in MAPMASK. Comparing the atom-tagged .map file and F obs(d n) − F obs(d 1) difference map at each dose, each refined atom was assigned a set of density-change values X. The maximum density-loss metric, D loss (units of e Å−3), was calculated to quantify the per-atom electron-density decay at each dose, assigned as the absolute magnitude of the most negative Fourier difference map voxel value in a local volume around each atom as defined by the set X. Model system calculation    Model calculations were run for the simple amino acids glutamate and aspartate. In order to avoid decarboxylation at the C-terminus instead of the side chain on the Cα atom, the C-terminus of each amino acid was methylated. While the structures of the closed shell acids are well known, the same is not true of those in the oxidized state. The quantum-chemical calculations employed were chosen to provide a satisfactory description of the structure of such radical species and also provide a reliable estimation of the relative C—C(O2) bond strengths, which are otherwise not available. Structures of methyl-terminated (at the N- and C-termini) carboxylates were determined using analytic energy gradients with density functional theory (B3LYP functional; Becke, 1993) and a flexible basis set of polarized valence triple-zeta size with diffuse functions on the non-H atoms [6-311+G(d,p)] in the Gaussian 09 computational chemistry package (Frisch et al., 2009). The stationary points obtained were characterized as at least local minima by examination of the associated analytic Hessian. Effects of the medium were modelled using a dielectric cavity approach (Tomasi et al., 1999) parameterized for water. Results    Per-atom quantification of electron density    To quantify the exact effects of nucleic acid binding to a protein on SRD susceptibility, a high-throughput and automated pipeline was created to systematically calculate the electron-density change for every refined atom within the TRAP–RNA structure as a function of dose. This provides an atom-specific quantification of density–dose dynamics, which was previously lacking within the field. Previous studies have characterized SRD sites by reporting magnitudes of F obs(d n) − F obs(d 1) Fourier difference map peaks in terms of the sigma (σ) contour level (the number of standard deviations from the mean map electron-density value) at which peaks become visible. However, these σ levels depend on the standard deviation values of the map, which can deviate between data sets, and are thus unsuitable for quantitative comparison of density between different dose data sets. Instead, we use here a maximum density-loss metric (D loss), which is the per-atom equivalent of the magnitude of these negative Fourier difference map peaks in units of e Å−3. Large positive D loss values indicate radiation-induced atomic disordering reproducibly throughout the unit cells with respect to the initial low-dose data set. For each TRAP–RNA data set, the D loss metric successfully identified the recognized forms of protein SRD (Fig. 2 ▸ a), with clear Glu and Asp side-chain decarboxylation even in the first difference map calculated (3.9 MGy; Fig. 3 ▸ a). The main sequence of TRAP does not contain any Trp and Cys residues (and thus contains no disulfide bonds). The substrate Trp amino-acid ligands also exhibited disordering of the free terminal carboxyl groups at higher doses (Fig. 2 ▸ a); however, no clear Fourier difference peaks could be observed visually. Even for radiation-insensitive residues (e.g. Gly) the average D loss increases with dose: this is the effect of global radiation damage, since as dose increases the electron density associated with each refined atom becomes weaker as the atomic occupancy decreases (Fig. 2 ▸ b). Only Glu and Asp residues exhibit a rate of D loss increase that consistently exceeds the average decay (Fig. 2 ▸ b, dashed line) at each dose. Additionally, the density surrounding ordered solvent molecules was determined to significantly diminish with increasing dose (Fig. 2 ▸ b). The rate of D loss (attributed to side-chain decarboxylation) was consistently larger for Glu compared with Asp residues over the large dose range (Fig. 2 ▸ b and Supplementary Fig. S3); this observation is consistent with our calculations on model systems (see above) that suggest that, without considering differential hydrogen-bonding environments, CO2 loss is more exothermic by around 8 kJ mol−1 from oxidized Glu residues than from their Asp counterparts. RNA is less susceptible to electron-density loss than protein within the TRAP–RNA complex    Visual inspection of Fourier difference maps illustrated the clear lack of RNA electron-density degradation with increasing dose compared with the obvious protein damage manifestations (Figs. 3 ▸ b and 3 ▸ c). Only at the highest doses investigated (\u003e20 MGy) was density loss observed at the RNA phosphate and C—O bonds of the phosphodiester backbone. However, the median D loss was lower by a factor of \u003e2 for RNA P atoms than for Glu and Asp side-chain groups at 25.0 MGy (Supplementary Fig. S4), and furthermore could not be numerically distinguished from Gly Cα atoms within TRAP, which are not radiation-sensitive at the doses tested here (Supplementary Fig. S3). RNA binding protects radiation-sensitive residues    For the large number of acidic residues per TRAP ring (four Asp and six Glu residues per protein monomer), a strong dependence of decarboxylation susceptibility on local environment was observed (Fig. 4 ▸). For each Glu Cδ or Asp Cγ atom, D loss provided a direct measure of the rate of side-chain carboxyl-group disordering and subsequent decarboxylation. For acidic residues with no differing interactions between nonbound and bound TRAP (Fig. 4 ▸ a), similar damage was apparent between the two rings within the asymmetric unit, as expected. However, TRAP residues directly on the RNA-binding interfaces exhibited greater damage accumulation in nonbound TRAP (Fig. 4 ▸ b), and for residues at the ring–ring interfaces (where crystal contacts were detected) bound TRAP exhibited enhanced SRD accumulation (Fig. 4 ▸ c). Three acidic residues (Glu36, Asp39 and Glu42) are involved in RNA interactions within each of the 11 TRAP ring subunits, and Fig. 5 ▸ shows their density changes with increasing dose. Hotelling’s T-squared test (the multivariate counterpart of Student’s t-test) was used to reject the null hypothesis that the means of the D loss metric were equal for the bound and nonbound groups in Fig. 5 ▸. A significant reduction in D loss is seen for Glu36 in RNA-bound compared with nonbound TRAP, indicative of a lower rate of side-chain decarboxylation (Fig. 5 ▸ a; p = 6.06 × 10−5). For each TRAP ring subunit, the Glu36 side-chain carboxyl group accepts a pair of hydrogen bonds from the two N atoms of the G3 RNA base. In our analysis, Asp39 in the TRAP–(GAGUU)10GAG structure appears to exhibit two distinct hydrogen bonds to the G1 base within each of the 11 TRAP–RNA interfaces, as does Glu36 to G3; however, the reduction in density disordering upon RNA binding is far less significant for Asp39 than for Glu36 (Fig. 5 ▸ b, p = 0.0925). RNA binding reduces radiation-induced disorder on the atomic scale    One oxygen (O∊1) of Glu42 appears to form a hydrogen bond to a nearby water within each TRAP RNA-binding pocket, with the other (O∊2) being involved in a salt-bridge interaction with Arg58 (Hopcroft et al., 2002; Antson et al., 1999). Salt-bridge interactions have previously been suggested to reduce the glutamate decarboxylation rate within the large (∼62.4 kDa) myrosinase protein structure (Burmeister, 2000). A significant difference was observed between the D loss dynamics for the nonbound/bound Glu42 O∊1 atoms (Fig. 5 ▸ c; p = 0.007) but not for the Glu42 O∊2 atoms (Fig. 5 ▸ d; p = 0.239), indicating that the stabilizing strength of this salt-bridge interaction was conserved upon RNA binding and that the water-mediated hydrogen bond had a greater relative susceptibility to atomic disordering in the absence of RNA. The density-change dynamics were statistically indistinguishable between bound and nonbound TRAP for each Glu42 carboxyl group Cδ atom (p = 0.435), indicating that upon RNA binding the conserved salt-bridge interaction ultimately dictated the overall Glu42 decarboxylation rate. The RNA-stabilizing effect was not restricted to radiation-sensitive acidic residues. The side chain of Phe32 stacks against the G3 base within the 11 TRAP RNA-binding interfaces (Antson et al., 1999). With increasing dose, the D loss associated with the Phe32 side chain was significantly reduced upon RNA binding (Fig. 5 ▸ e; Phe32 Cζ; p = 0.0014), an indication that radiation-induced conformation disordering of Phe32 had been reduced. The extended aliphatic Lys37 side chain stacks against the nearby G1 base, making a series of nonpolar contacts within each RNA-binding interface. The D loss for Lys37 side-chain atoms was also reduced when stacked against the G1 base (Fig. 5 ▸ f; p = 0.0243 for Lys37 C∊ atoms). Representative Phe32 and Lys37 atoms were selected to illustrate these trends. Discussion    Here, MX radiation-induced specific structural changes within the large TRAP–RNA assembly over a large dose range (1.3–25.0 MGy) have been analysed using a high-throughput quantitative approach, providing a measure of the electron-density distribution for each refined atom with increasing dose, D loss. Compared with previous studies, the results provide a further step in the detailed characterization of SRD effects in MX. Our method­ology, which eliminated tedious and error-prone visual inspection, permitted the determination on a per-atom basis of the most damaged sites, as characterized by F obs(d n) − F obs(d 1) Fourier difference map peaks between successive data sets collected from the same crystal. Here, it provided the precision required to quantify the role of RNA in the damage susceptibilities of equivalent atoms between RNA-bound and nonbound TRAP, but it is applicable to any MX SRD study. The RNA was found to be substantially more radiation-resistant than the protein, even at the highest doses investigated (∼25.0 MGy), which is in strong concurrence with our previous SRD investigation of the C.Esp1396I protein–DNA complex (Bury et al., 2015). Consistent with that study, at high doses of above ∼20 MGy, F obs(d n) − F obs(d 1) map density was detected around P, O3′ and O5′ atoms of the RNA backbone, with no significant difference density localized to RNA ribose and basic subunits. RNA backbone disordering thus appears to be the main radiation-induced effect in RNA, with the protein–base interactions maintained even at high doses (\u003e20 MGy). The U4 phosphate exhibited marginally larger D loss values above 20 MGy than G1, A2 and G3 (Supplementary Fig. S4). Since U4 is the only refined nucleotide not to exhibit significant base–protein interactions around TRAP (with a water-mediated hydrogen bond detected in only three of the 11 subunits and a single Arg58 hydrogen bond suggested in a further four subunits), this increased U4 D loss can be explained owing to its greater flexibility. At 25.0 MGy, the magnitude of the RNA backbone D loss was of the same order as for the radiation-insensitive Gly Cα atoms and on average less than half that of the acidic residues of the protein (Supplementary Fig. S3). Consequently, no clear single-strand breaks could be located, and since RNA-binding within the current TRAP–(GAGUU)10GAG complex is mediated predominantly through base–protein interactions, the biological integrity of the RNA complex was dictated by the rate at which protein decarboxylation occurred. RNA interacting with TRAP was shown to offer significant protection against radiation-induced structural changes. Both Glu36 and Asp39 bind directly to RNA, each through two hydrogen bonds to guanine bases (G3 and G1, respectively). However, compared with Asp39, Glu36 is strikingly less decarboxylated when bound to RNA (Fig. 4 ▸). This is in good agreement with previous mutagenesis and nucleoside analogue studies (Elliott et al., 2001), which indicated that the G1 nucleotide does not bind to TRAP as strongly as do A2 and G3, and plays little role in the high RNA-binding affinity of TRAP (K d ≃ 1.1 ± 0.4 nM). For Glu36 and Asp39, no direct quantitative correlation could be established between hydrogen-bond length and D loss (linear R 2 of \u003c0.23 for all doses; Supplementary Fig. S5). Thus, another factor must be responsible for this clear reduction in Glu36 CO2 decarboxyl­ation in RNA-bound TRAP. The Glu36 carboxyl side chain also potentially forms hydrogen bonds to His34 and Lys56, but since these interactions are conserved irrespective of G3 nucleotide binding, this cannot directly account for the stabilization effect on Glu36 in RNA-bound TRAP. Radiation-induced decarboxylation has been proposed to be mediated by preferential positive-hole migration to the side-chain carboxyl group, with rapid proton transfer trapping the hole at the carboxyl group (Burmeister, 2000; Symons, 1997):where the forward rate is K 1 and the backward rate is K −1, where the forward rate is K 2. When bound to RNA, the average solvent-accessible area of the Glu36 side-chain O atoms is reduced from ∼15 to 0 Å2. We propose that with no solvent accessibility Glu36 decarboxylation is inhibited, since the CO2-formation rate K 2 is greatly reduced, and suggest that steric hindrance prevents each radicalized Glu36 CO2 group from achieving the planar conformation required for complete dissociation from TRAP. The electron-recombination rate K −1 remains high, however, owing to rapid electron migration through the protein–RNA complex to refill the Glu36 positive hole (the precursor for Glu decarboxylation). Upon RNA binding, the Asp39 side-chain carboxyl group solvent-accessible area changes from ∼75 to 35 Å2, still allowing a high CO2-formation rate K 2. Previous studies have reported inconsistent results concerning the dependence of the acidic residue decarboxylation rate on solvent accessibility (Weik et al., 2000; Fioravanti et al., 2007; Gerstel et al., 2015). The prevalence of radical attack from solvent channels surrounding the protein in the crystal is a questionable cause, considering previous observations indicating that the strongly oxidizing hydroxyl radical is immobile at 100 K (Allan et al., 2013; Owen et al., 2012). Furthermore, the suggested electron hole-trapping mechanism which induces decarboxylation within proteins at 100 K has no clear mechanistic dependence on the solvent-accessible area of each carboxyl group. By comparing equivalent acidic residues with and without RNA, we have now deconvoluted the role of solvent accessibility from other local protein environment factors, and thus propose a suitable mechanism by which exceptionally low solvent accessibility can reduce the rate of decarboxylation. Overall, no direct correlation between solvent accessibility and decarboxylation susceptibility was observed, but it is very clear that inaccessible residues are protected. Apart from these RNA-binding interfaces, RNA binding was seen to enhance decarboxylation for residues Glu50, Glu71 and Glu73, all of which are involved in crystal contacts between TRAP rings (Fig. 4 ▸ c). However, for each of these residues the exact crystal contacts are not preserved between bound and nonbound TRAP or even between monomers within one TRAP ring. For example, in bound TRAP, Glu73 hydrogen-bonds to a nearby lysine on each of the 11 subunits, whereas in nonbound TRAP no such interaction exists and Glu73 interacts with a variable number of refined waters in each subunit. Thus, the dependence of decarboxylation rates on these interactions could not be established. Radiation-induced side-chain conformational changes have been poorly characterized in previous SRD investigations owing to their strong dependence on packing density and geometric strain. Such structural changes are known to have significant roles within enzymatic pathways, and experimenters must be aware of these possible confounding factors when assigning true functional mechanisms using MX. Our results show that RNA binding to TRAP physically stabilizes non-acidic residues within the TRAP macromolecule, most notably Lys37 and Phe32, which stack against the G1 and G3 bases, respectively. It has been suggested (Burmeister, 2000) that Tyr residues can lose their aromatic –OH group owing to radiation-induced effects; however, no energetically favourable pathway for –OH cleavage exists and this has not been detected in aqueous radiation-chemistry studies. In TRAP, D loss increased at a similar rate for both the Tyr O atoms and aromatic ring atoms, suggesting that full ring conformational disordering is more likely. Indeed, no convincing reproducible Fourier difference peaks above the background map noise were observed around any Tyr terminal –OH groups. The RNA-stabilization effects on protein are observed at short ranges and are restricted to within the RNA-binding interfaces around the TRAP ring. For example, Asp17 is located ∼6.8 Å from the G1 base, outside the RNA-binding interfaces, and has indistinguishable Cγ atom D loss dose-dynamics between RNA-bound and nonbound TRAP (p \u003e 0.9). An increase in the dose at which functionally important residues remain intact has biological ramifications for understanding the mechanisms at which ionizing radiation damage is mitigated within naturally forming DNA–protein and RNA–protein complexes. Observations of lower protein radiation-sensitivity in DNA-bound forms have been recorded in solution at RT at much lower doses (∼1 kGy) than those used for typical MX experiments [e.g. an oestrogen response element–receptor complex (Stísová et al., 2006) and a DNA glycosylase and its abasic DNA target site (Gillard et al., 2004)]. In these studies, the main damaging species is predicted to be the oxidizing hydroxyl radical produced through solvent irradiation, which is known to add to double covalent bonds within both DNA and RNA bases to induce strand breaks and base modification (Spotheim-Maurizot \u0026 Davídková, 2011; Chance et al., 1997). It was suggested that physical screening of DNA by protein shielded the DNA–protein interaction sites from radical damage, yielding an extended life-dose for the nucleoprotein complex compared with separate protein and DNA constituents at RT. However, in the current MX study at 100 K, the main damaging species are believed to be migrating LEEs and holes produced directly within the protein–RNA components or in closely associated solvent. The results presented here suggest that biologically relevant nucleoprotein complexes also exhibit prolonged life-doses under the effect of LEE-induced structural changes, involving direct physical protection of key RNA-binding residues. Such reduced radiation-sensitivity in this case ensures that the interacting protein remains bound long enough to the RNA to complete its function, even whilst exposed to ionizing radiation. Within the nonbound TRAP macromolecule, the acidic residues within the unoccupied RNA-binding interfaces (Asp39, Glu36, Glu42) are notably amongst the most susceptible residues within the asymmetric unit (Fig. 4 ▸). When exposed to X-rays, these residues will be preferentially damaged by X-rays and subsequently reduce the affinity with which TRAP binds to RNA. Within the cellular environment, this mechanism could reduce the risk that radiation-damaged proteins might bind to RNA, thus avoiding the detrimental introduction of incorrect DNA-repair, transcriptional and base-modification pathways. The Python scripts written to calculate the per atom D loss metric are available from the authors on request. Related literature    The following references are cited in the Supporting Information for this article: Chen et al. (2010). Supplementary Material References Adams, P. D. et al. (2010). Acta Cryst. D66, 213–221. Alizadeh, E. \u0026 Sanche, L. (2014). Eur. Phys. J. D, 68, 97. Allan, E. G., Kander, M. C., Carmichael, I. \u0026 Garman, E. F. (2013). J. Synchrotron Rad. 20, 23–36. Antson, A. A., Dodson, E. J., Dodson, G., Greaves, R. B., Chen, X. \u0026 Gollnick, P. (1999). Nature (London), 401, 235–242. Becke, A. D. (1993). J. Chem. Phys. 98, 5648–5652. Bourenkov, G. P. \u0026 Popov, A. N. (2010). Acta Cryst. D66, 409–419. Burmeister, W. P. (2000). Acta Cryst. D56, 328–341. Bury, C., Garman, E. F., Ginn, H. M., Ravelli, R. B. G., Carmichael, I., Kneale, G. \u0026 McGeehan, J. E. (2015). J. Synchrotron Rad. 22, 213–224. Chance, M. R., Sclavi, B., Woodson, S. A. \u0026 Brenowitz, M. (1997). Structure, 5, 865–869. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. \u0026 Richardson, D. C. (2010). Acta Cryst. D66, 12–21. Dubnovitsky, A. P., Ravelli, R. B. G., Popov, A. N. \u0026 Papageorgiou, A. C. (2005). Protein Sci. 14, 1498–1507. Elliott, M. B., Gottlieb, P. A. \u0026 Gollnick, P. (2001). RNA, 7, 85–93. Emsley, P., Lohkamp, B., Scott, W. G. \u0026 Cowtan, K. (2010). Acta Cryst. D66, 486–501. Evans, P. R. \u0026 Murshudov, G. N. (2013). Acta Cryst. D69, 1204–1214. Fioravanti, E., Vellieux, F. M. D., Amara, P., Madern, D. \u0026 Weik, M. (2007). J. Synchrotron Rad. 14, 84–91. Frisch, M. J. et al. (2009). Gaussian 09. Gaussian Inc., Wallingford, Connecticut, USA. Garman, E. F. (2010). Acta Cryst. D66, 339–351. Gerstel, M., Deane, C. M. \u0026 Garman, E. F. (2015). J. Synchrotron Rad. 22, 201–212. Gillard, N., Begusova, M., Castaing, B. \u0026 Spotheim-Maurizot, M. (2004). Radiat. Res. 162, 566–571. Holton, J. M. (2007). J. Synchrotron Rad. 14, 51–72. Holton, J. M. (2009). J. Synchrotron Rad. 16, 133–142. Hopcroft, N. H., Wendt, A. L., Gollnick, P. \u0026 Antson, A. A. (2002). Acta Cryst. D58, 615–621. Jones, G. D., Lea, J. S., Symons, M. C. \u0026 Taiwo, F. A. (1987). Nature (London), 330, 772–773. Leslie, A. G. W. \u0026 Powell, H. R. (2007). Evolving Methods for Macromolecular Crystallography, edited by R. J. Read \u0026 J. L. Sussman, pp. 41–51. Dordrecht: Springer. Liebschner, D., Rosenbaum, G., Dauter, M. \u0026 Dauter, Z. (2015). Acta Cryst. D71, 772–778. Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H. \u0026 Kouyama, T. (2002). J. Mol. Biol. 324, 469–481. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. \u0026 Read, R. J. (2007). J. Appl. Cryst. 40, 658–674. McGeehan, J. E., Streeter, S. D., Thresh, S. J., Ball, N., Ravelli, R. B. G. \u0026 Kneale, G. G. (2008). Nucleic Acids Res. 36, 4778–4787. Murray, J. \u0026 Garman, E. (2002). J. Synchrotron Rad. 9, 347–354. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. \u0026 Vagin, A. A. (2011). Acta Cryst. D67, 355–367. O’Neill, P., Stevens, D. L. \u0026 Garman, E. (2002). J. Synchrotron Rad. 9, 329–332. Owen, R. L., Axford, D., Nettleship, J. E., Owens, R. J., Robinson, J. I., Morgan, A. W., Doré, A. S., Lebon, G., Tate, C. G., Fry, E. E., Ren, J., Stuart, D. I. \u0026 Evans, G. (2012). Acta Cryst. D68, 810–818. Owen, R. L., Rudiño-Piñera, E. \u0026 Garman, E. F. (2006). Proc. Natl Acad. Sci. USA, 103, 4912–4917. Ptasińska, S. \u0026 Sanche, L. (2007). Phys. Rev. E, 75, 031915. Ravelli, R. B. G. \u0026 McSweeney, S. M. (2000). Structure, 8, 315–328. Shimizu, N., Hirata, K., Hasegawa, K., Ueno, G. \u0026 Yamamoto, M. (2007). J. Synchrotron Rad. 14, 4–10. Simons, J. (2006). Acc. Chem. Res. 39, 772–779. Spotheim-Maurizot, M. \u0026 Davídková, M. (2011). Mutat. Res. 711, 41–48. Stísová, V., Goffinont, S., Spotheim-Maurizot, M. \u0026 Davídková, M. (2006). Radiat. Prot. Dosimetry, 122, 106–109. Symons, M. C. R. (1997). Free Radical Biol. Med. 22, 1271–1276. Ten Eyck, L. F. (1973). Acta Cryst. A29, 183–191. Tomasi, J., Mennucci, B. \u0026 Cancès, E. (1999). J. Mol. Struct. 464, 211–226. Weik, M., Ravelli, R. B. G., Kryger, G., McSweeney, S., Raves, M. L., Harel, M., Gros, P., Silman, I., Kroon, J. \u0026 Sussman, J. L. (2000). Proc. Natl Acad. Sci. USA, 97, 623–628. Winn, M. D. et al. (2011). Acta Cryst. D67, 235–242. Yano, J., Kern, J., Irrgang, K. D., Latimer, M. J., Bergmann, U., Glatzel, P., Pushkar, Y., Biesiadka, J., Loll, B., Sauer, K., Messinger, J., Zouni, A. \u0026 Yachandra, V. K. (2005). Proc. Natl Acad. Sci. USA, 102, 12047–12052. Zeldin, O. B., Brockhauser, S., Bremridge, J., Holton, J. M. \u0026 Garman, E. F. (2013). Proc. Natl Acad. Sci. USA, 110, 20551–20556. Zeldin, O. B., Gerstel, M. \u0026 Garman, E. F. (2013). J. Appl. Cryst. 46, 1225–1230. The TRAP–(GAGUU)10GAG complex asymmetric unit (PDB entry 1gtf; Hopcroft et al., 2002). Bound tryptophan ligands are represented as coloured spheres. RNA is shown is yellow. (a) Electron-density loss sites as indicated by D\nloss in the TRAP–RNA complex crystal by residue/nucleotide type for five doses [sites determined above the 4× average D\nloss threshold, calculated over the TRAP–RNA structure for the first difference map: F\nobs(d\n2) − F\nobs(d\n1)]. Cumulative frequencies are normalized to both the total number of non-H atoms per residue/nucleotide and the total number of that residue/nucleotide type present. (b) Average D\nloss for each residue/nucleotide type with respect to the DWD (diffraction-weighted dose; Zeldin, Brock­hauser et al., 2013). 95% confidence intervals (CI) are shown. Only a subset of key TRAP residue types are included. The average D\nloss (calculated over the whole TRAP asymmetric unit) is shown at each dose (dashed line). \nF\nobs(d\nn) − F\nobs(d\n1) Fourier difference maps for (a) n = 2 (3.9 MGy), (b) n = 3 (6.5 MGy) and (c) n = 7 (16.7 MGy) contoured at ±4σ (a) and ±3.5σ (b, c). In (a) clear difference density is observed around the Glu42 carboxyl side chain in chain H, within the lowest dose difference map at d\n2 = 3.9 MGy. Radiation-induced protein disordering is evident across the large dose range (b, c); in comparison, no clear deterioration of the RNA density was observed. \nD\nloss calculated for all side-chain carboxyl group Glu Cδ and Asp Cγ atoms within the TRAP–RNA complex for a dose of 19.3 MGy (d\n8). Residues have been grouped by amino-acid number, and split into bound and nonbound groupings, with each bar representing the mean calculated over 11 equivalent atoms around a TRAP ring. Whiskers indicate 95% CI. The D\nloss behaviour shown here was consistently exhibited across the entire investigated dose range. \nD\nloss against dose for (a) Glu36 Cδ, (b) Asp39 Cγ, (c) Glu42 O∊1, (d) Glu42 O∊2, (e) Phe32 Cζ and (f) Lys37 C∊ atoms. 95% CI are included for each set of 11 equivalent atoms grouped as bound/nonbound. RNA-binding interface interactions are shown for TRAP chain N, with the F\nobs(d\n7) − F\nobs(d\n1) Fourier difference map (dose 16.7 MGy) overlaid and contoured at a ±4σ level.","denotations":[{"span":{"begin":0,"end":3},"obj":"0.9980228,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"1"},{"span":{"begin":15,"end":28},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T10:34:01Z","id":"760"},{"span":{"begin":111,"end":122},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:04:56Z","id":"839"},{"span":{"begin":219,"end":222},"obj":"0.9902272,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"3"},{"span":{"begin":252,"end":294},"obj":"0.9882428,experimental_method,cleaner0,2023-07-05T12:16:13Z,MESH:","id":"4"},{"span":{"begin":339,"end":392},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:16:36Z","id":"887"},{"span":{"begin":431,"end":470},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T10:26:50Z","id":"725"},{"span":{"begin":803,"end":811},"obj":"0.93006164,evidence,cleaner0,2023-07-05T10:27:59Z,DUMMY:","id":"7"},{"span":{"begin":960,"end":984},"obj":"0.9697803,evidence,cleaner0,2023-07-05T10:28:01Z,DUMMY:","id":"8"},{"span":{"begin":1157,"end":1160},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"763"},{"span":{"begin":1234,"end":1269},"obj":"0.9563537,protein_type,cleaner0,2023-07-05T12:26:59Z,MESH:","id":"11"},{"span":{"begin":1271,"end":1275},"obj":"0.53643787,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"12"},{"span":{"begin":1277,"end":1285},"obj":"0.99148065,protein_state,cleaner0,2023-07-05T12:33:37Z,DUMMY:","id":"13"},{"span":{"begin":1304,"end":1307},"obj":"0.9971852,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"15"},{"span":{"begin":1375,"end":1378},"obj":"0.99032986,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"16"},{"span":{"begin":1496,"end":1500},"obj":"0.937143,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"17"},{"span":{"begin":1563,"end":1568},"obj":"0.9731102,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"18"},{"span":{"begin":1569,"end":1572},"obj":"0.99720335,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"19"},{"span":{"begin":1632,"end":1635},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"669"},{"span":{"begin":1720,"end":1724},"obj":"0.8899272,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"20"},{"span":{"begin":1725,"end":1729},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"821"},{"span":{"begin":1782,"end":1785},"obj":"0.9860465,residue_name,cleaner0,2023-07-05T10:28:06Z,SO:","id":"21"},{"span":{"begin":1790,"end":1793},"obj":"0.9869811,residue_name,cleaner0,2023-07-05T10:28:09Z,SO:","id":"22"},{"span":{"begin":1816,"end":1819},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"670"},{"span":{"begin":1923,"end":1942},"obj":"0.9977442,site,cleaner0,2023-07-05T12:01:06Z,SO:","id":"23"},{"span":{"begin":2087,"end":2090},"obj":"0.9823989,residue_name,cleaner0,2023-07-05T10:28:11Z,SO:","id":"24"},{"span":{"begin":2095,"end":2098},"obj":"0.9763282,residue_name,cleaner0,2023-07-05T10:28:13Z,SO:","id":"25"},{"span":{"begin":2116,"end":2119},"obj":"0.652342,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"26"},{"span":{"begin":2146,"end":2162},"obj":"0.9961912,evidence,cleaner0,2023-07-05T10:28:04Z,DUMMY:","id":"27"},{"span":{"begin":2340,"end":2363},"obj":"0.8348757,experimental_method,cleaner0,2023-07-05T10:28:23Z,MESH:","id":"28"},{"span":{"begin":2370,"end":2400},"obj":"0.98041725,experimental_method,cleaner0,2023-07-05T10:28:25Z,MESH:","id":"29"},{"span":{"begin":2402,"end":2404},"obj":"0.56438595,experimental_method,cleaner0,2023-07-05T10:28:29Z,MESH:","id":"30"},{"span":{"begin":2630,"end":2638},"obj":"0.9865131,evidence,cleaner0,2023-07-05T10:28:34Z,DUMMY:","id":"31"},{"span":{"begin":2888,"end":2890},"obj":"0.9509965,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"32"},{"span":{"begin":3283,"end":3302},"obj":"0.9363032,evidence,cleaner0,2023-07-05T12:19:18Z,DUMMY:","id":"33"},{"span":{"begin":3534,"end":3536},"obj":"0.96844155,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"34"},{"span":{"begin":3732,"end":3739},"obj":"0.91692525,evidence,cleaner0,2023-07-05T10:31:01Z,DUMMY:","id":"35"},{"span":{"begin":3793,"end":3818},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:19:00Z","id":"892"},{"span":{"begin":3820,"end":3823},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:19:10Z","id":"893"},{"span":{"begin":3844,"end":3871},"obj":"0.9674265,evidence,cleaner0,2023-07-05T10:31:05Z,DUMMY:","id":"36"},{"span":{"begin":3988,"end":3990},"obj":"0.28211054,chemical,cleaner0,2023-07-05T10:29:47Z,CHEBI:","id":"37"},{"span":{"begin":3999,"end":4015},"obj":"0.9843067,chemical,cleaner0,2023-07-05T10:29:51Z,CHEBI:","id":"38"},{"span":{"begin":4143,"end":4150},"obj":"0.9706023,evidence,cleaner0,2023-07-05T10:31:07Z,DUMMY:","id":"39"},{"span":{"begin":4319,"end":4333},"obj":"ptm,MESH:,cleaner0,2023-07-05T10:30:47Z","id":"757"},{"span":{"begin":5120,"end":5133},"obj":"0.9724948,experimental_method,cleaner0,2023-07-05T10:31:22Z,MESH:","id":"45"},{"span":{"begin":5134,"end":5144},"obj":"0.9942268,evidence,cleaner0,2023-07-05T12:19:53Z,DUMMY:","id":"46"},{"span":{"begin":5267,"end":5287},"obj":"0.9978055,site,cleaner0,2023-07-05T12:01:17Z,SO:","id":"47"},{"span":{"begin":5472,"end":5495},"obj":"0.99299383,experimental_method,cleaner0,2023-07-05T10:31:25Z,MESH:","id":"48"},{"span":{"begin":5527,"end":5545},"obj":"0.84919345,protein_type,cleaner0,2023-07-05T10:31:44Z,MESH:","id":"49"},{"span":{"begin":5777,"end":5788},"obj":"0.99806416,site,cleaner0,2023-07-05T12:01:21Z,SO:","id":"50"},{"span":{"begin":5792,"end":5822},"obj":"0.9870368,protein_type,cleaner0,2023-07-05T10:31:34Z,MESH:","id":"51"},{"span":{"begin":5928,"end":5939},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T10:32:31Z","id":"758"},{"span":{"begin":6066,"end":6079},"obj":"0.5266972,complex_assembly,cleaner0,2023-07-05T11:49:23Z,GO:","id":"56"},{"span":{"begin":6208,"end":6211},"obj":"0.6261449,chemical,cleaner0,2023-07-05T10:36:34Z,CHEBI:","id":"57"},{"span":{"begin":6348,"end":6351},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"764"},{"span":{"begin":6384,"end":6397},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T10:33:26Z","id":"759"},{"span":{"begin":6406,"end":6416},"obj":"0.9936459,evidence,cleaner0,2023-07-05T12:19:56Z,DUMMY:","id":"59"},{"span":{"begin":6472,"end":6474},"obj":"0.9480319,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"60"},{"span":{"begin":6552,"end":6562},"obj":"0.9201258,evidence,cleaner0,2023-07-05T12:19:59Z,DUMMY:","id":"61"},{"span":{"begin":6613,"end":6627},"obj":"0.78504515,complex_assembly,cleaner0,2023-07-05T10:33:41Z,GO:","id":"62"},{"span":{"begin":7303,"end":7306},"obj":"0.9642742,chemical,cleaner0,2023-07-05T10:36:34Z,CHEBI:","id":"65"},{"span":{"begin":7464,"end":7467},"obj":"0.94849676,chemical,cleaner0,2023-07-05T10:36:34Z,CHEBI:","id":"66"},{"span":{"begin":7639,"end":7675},"obj":"0.99424225,experimental_method,cleaner0,2023-07-05T10:34:36Z,MESH:","id":"67"},{"span":{"begin":7834,"end":7837},"obj":"0.8569334,chemical,cleaner0,2023-07-05T10:36:34Z,CHEBI:","id":"68"},{"span":{"begin":7954,"end":7970},"obj":"0.97740066,site,cleaner0,2023-07-05T12:01:27Z,SO:","id":"69"},{"span":{"begin":8216,"end":8228},"obj":"0.92757994,experimental_method,cleaner0,2023-07-05T10:35:56Z,MESH:","id":"70"},{"span":{"begin":8276,"end":8285},"obj":"taxonomy_domain,DUMMY:,cleaner0,2023-07-05T10:35:49Z","id":"761"},{"span":{"begin":8294,"end":8297},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"765"},{"span":{"begin":8307,"end":8317},"obj":"0.99454117,complex_assembly,cleaner0,2023-07-05T12:31:03Z,GO:","id":"73"},{"span":{"begin":8489,"end":8492},"obj":"0.99493873,chemical,cleaner0,2023-07-05T10:36:33Z,CHEBI:","id":"74"},{"span":{"begin":8504,"end":8511},"obj":"0.9964142,evidence,cleaner0,2023-07-05T12:20:04Z,DUMMY:","id":"75"},{"span":{"begin":8624,"end":8639},"obj":"structure_element,SO:,cleaner0,2023-07-05T10:36:28Z","id":"762"},{"span":{"begin":8654,"end":8657},"obj":"0.9971282,chemical,cleaner0,2023-07-05T10:36:34Z,CHEBI:","id":"78"},{"span":{"begin":8704,"end":8714},"obj":"0.99455875,complex_assembly,cleaner0,2023-07-05T12:31:03Z,GO:","id":"80"},{"span":{"begin":8852,"end":8855},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"766"},{"span":{"begin":9094,"end":9101},"obj":"0.9853733,evidence,cleaner0,2023-07-05T12:20:08Z,DUMMY:","id":"82"},{"span":{"begin":9178,"end":9186},"obj":"0.98737174,protein_state,cleaner0,2023-07-05T12:33:43Z,DUMMY:","id":"83"},{"span":{"begin":9187,"end":9190},"obj":"0.9977902,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"84"},{"span":{"begin":9269,"end":9283},"obj":"0.9718507,experimental_method,cleaner0,2023-07-05T12:16:48Z,MESH:","id":"85"},{"span":{"begin":9355,"end":9366},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:04:56Z","id":"840"},{"span":{"begin":9376,"end":9411},"obj":"0.9377823,protein_type,cleaner0,2023-07-05T12:27:03Z,MESH:","id":"88"},{"span":{"begin":9413,"end":9417},"obj":"0.8530336,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"89"},{"span":{"begin":9419,"end":9427},"obj":"0.9948477,protein_state,cleaner0,2023-07-05T11:51:21Z,DUMMY:","id":"90"},{"span":{"begin":9436,"end":9439},"obj":"0.99753857,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"91"},{"span":{"begin":9449,"end":9461},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:38:29Z","id":"776"},{"span":{"begin":9503,"end":9507},"obj":"0.9524646,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"93"},{"span":{"begin":9533,"end":9541},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:54Z","id":"882"},{"span":{"begin":9559,"end":9563},"obj":"0.5846764,structure_element,cleaner0,2023-07-05T11:58:12Z,SO:","id":"94"},{"span":{"begin":9627,"end":9630},"obj":"0.9860402,evidence,cleaner0,2023-07-05T12:20:10Z,DUMMY:","id":"95"},{"span":{"begin":9644,"end":9647},"obj":"0.9952761,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"96"},{"span":{"begin":9671,"end":9687},"obj":"0.9207858,structure_element,cleaner0,2023-07-05T10:47:16Z,SO:","id":"97"},{"span":{"begin":9714,"end":9732},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:54:57Z","id":"820"},{"span":{"begin":9789,"end":9799},"obj":"0.90775585,chemical,cleaner0,2023-07-05T12:14:09Z,CHEBI:","id":"100"},{"span":{"begin":9822,"end":9839},"obj":"0.99550605,species,cleaner0,2023-07-05T10:37:26Z,MESH:","id":"101"},{"span":{"begin":9871,"end":9880},"obj":"0.9971539,evidence,cleaner0,2023-07-05T12:20:16Z,DUMMY:","id":"102"},{"span":{"begin":9899,"end":9907},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:39:38Z","id":"778"},{"span":{"begin":9974,"end":9979},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:39:55Z","id":"779"},{"span":{"begin":10077,"end":10079},"obj":"0.947729,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"107"},{"span":{"begin":10119,"end":10127},"obj":"0.98999834,complex_assembly,cleaner0,2023-07-05T10:38:43Z,GO:","id":"108"},{"span":{"begin":10128,"end":10135},"obj":"0.9876061,evidence,cleaner0,2023-07-05T10:40:23Z,DUMMY:","id":"109"},{"span":{"begin":10297,"end":10318},"obj":"0.99650353,evidence,cleaner0,2023-07-05T10:40:25Z,DUMMY:","id":"114"},{"span":{"begin":10329,"end":10338},"obj":"0.99333715,site,cleaner0,2023-07-05T12:01:33Z,SO:","id":"115"},{"span":{"begin":10394,"end":10417},"obj":"0.9945757,evidence,cleaner0,2023-07-05T10:40:28Z,DUMMY:","id":"116"},{"span":{"begin":10615,"end":10619},"obj":"0.9496573,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"117"},{"span":{"begin":10718,"end":10721},"obj":"0.99639255,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"118"},{"span":{"begin":10733,"end":10737},"obj":"0.9609993,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"119"},{"span":{"begin":18315,"end":18358},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T11:50:30Z","id":"819"},{"span":{"begin":18538,"end":18561},"obj":"0.993571,evidence,cleaner0,2023-07-05T12:20:24Z,DUMMY:","id":"279"},{"span":{"begin":18596,"end":18604},"obj":"0.9888622,complex_assembly,cleaner0,2023-07-05T10:38:43Z,GO:","id":"280"},{"span":{"begin":18605,"end":18614},"obj":"0.9903577,evidence,cleaner0,2023-07-05T12:20:28Z,DUMMY:","id":"281"},{"span":{"begin":18687,"end":18708},"obj":"0.82108414,evidence,cleaner0,2023-07-05T12:20:32Z,DUMMY:","id":"282"},{"span":{"begin":18793,"end":18802},"obj":"0.9954945,site,cleaner0,2023-07-05T12:01:39Z,SO:","id":"283"},{"span":{"begin":18830,"end":18882},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:01:56Z","id":"834"},{"span":{"begin":18899,"end":18904},"obj":"0.88435054,evidence,cleaner0,2023-07-05T12:20:37Z,DUMMY:","id":"286"},{"span":{"begin":18906,"end":18907},"obj":"0.58001226,evidence,cleaner0,2023-07-05T12:20:40Z,DUMMY:","id":"287"},{"span":{"begin":18938,"end":18957},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:03:31Z","id":"837"},{"span":{"begin":18967,"end":18998},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:03:02Z","id":"835"},{"span":{"begin":19046,"end":19047},"obj":"0.7078795,evidence,cleaner0,2023-07-05T12:20:44Z,DUMMY:","id":"289"},{"span":{"begin":19069,"end":19087},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:03:19Z","id":"836"},{"span":{"begin":19102,"end":19105},"obj":"0.9917287,evidence,cleaner0,2023-07-05T12:20:48Z,DUMMY:","id":"291"},{"span":{"begin":19199,"end":19206},"obj":"0.6958162,evidence,cleaner0,2023-07-05T12:20:51Z,DUMMY:","id":"292"},{"span":{"begin":19264,"end":19291},"obj":"0.9909112,evidence,cleaner0,2023-07-05T12:20:55Z,DUMMY:","id":"293"},{"span":{"begin":19293,"end":19299},"obj":"0.97732365,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"294"},{"span":{"begin":19361,"end":19398},"obj":"0.9871848,evidence,cleaner0,2023-07-05T12:21:00Z,DUMMY:","id":"295"},{"span":{"begin":19433,"end":19439},"obj":"0.98676395,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"296"},{"span":{"begin":19601,"end":19609},"obj":"0.96854377,complex_assembly,cleaner0,2023-07-05T10:38:43Z,GO:","id":"298"},{"span":{"begin":19624,"end":19637},"obj":"0.9839508,evidence,cleaner0,2023-07-05T12:21:04Z,DUMMY:","id":"299"},{"span":{"begin":19694,"end":19697},"obj":"0.98396283,experimental_method,cleaner0,2023-07-05T12:27:21Z,MESH:","id":"300"},{"span":{"begin":19723,"end":19726},"obj":"0.9861578,residue_name,cleaner0,2023-07-05T12:07:07Z,SO:","id":"301"},{"span":{"begin":19731,"end":19734},"obj":"0.98857224,residue_name,cleaner0,2023-07-05T10:42:18Z,SO:","id":"302"},{"span":{"begin":19780,"end":19794},"obj":"evidence,DUMMY:,melaniev@ebi.ac.uk,2023-07-06T15:26:33Z","id":"894"},{"span":{"begin":19850,"end":19854},"obj":"0.91976935,complex_assembly,cleaner0,2023-07-05T12:07:53Z,GO:","id":"304"},{"span":{"begin":19876,"end":19879},"obj":"0.9860378,residue_name,cleaner0,2023-07-05T10:42:35Z,SO:","id":"305"},{"span":{"begin":19884,"end":19887},"obj":"0.99085087,residue_name,cleaner0,2023-07-05T10:42:39Z,SO:","id":"306"},{"span":{"begin":19951,"end":19954},"obj":"0.9699916,chemical,cleaner0,2023-07-05T12:14:14Z,CHEBI:","id":"307"},{"span":{"begin":20086,"end":20110},"obj":"0.9950683,evidence,cleaner0,2023-07-05T12:21:30Z,DUMMY:","id":"308"},{"span":{"begin":20185,"end":20188},"obj":"0.97884846,residue_name,cleaner0,2023-07-05T10:42:43Z,SO:","id":"310"},{"span":{"begin":20202,"end":20208},"obj":"0.9714825,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"311"},{"span":{"begin":20305,"end":20321},"obj":"0.99046993,evidence,cleaner0,2023-07-05T12:21:33Z,DUMMY:","id":"312"},{"span":{"begin":20424,"end":20427},"obj":"0.98477256,residue_name,cleaner0,2023-07-05T12:07:11Z,SO:","id":"313"},{"span":{"begin":20432,"end":20435},"obj":"0.98784196,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"314"},{"span":{"begin":20463,"end":20469},"obj":"0.7084436,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"315"},{"span":{"begin":20715,"end":20721},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T10:43:57Z","id":"798"},{"span":{"begin":20793,"end":20796},"obj":"0.9841786,residue_name,cleaner0,2023-07-05T12:07:17Z,SO:","id":"317"},{"span":{"begin":20811,"end":20814},"obj":"0.9849412,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"318"},{"span":{"begin":21055,"end":21058},"obj":"0.993453,chemical,cleaner0,2023-07-05T12:14:18Z,CHEBI:","id":"319"},{"span":{"begin":21109,"end":21117},"obj":"0.9969453,protein_state,cleaner0,2023-07-05T12:31:56Z,DUMMY:","id":"320"},{"span":{"begin":21118,"end":21121},"obj":"0.98660594,residue_name,cleaner0,2023-07-05T12:07:19Z,SO:","id":"321"},{"span":{"begin":21147,"end":21150},"obj":"0.98063844,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"322"},{"span":{"begin":21189,"end":21192},"obj":"0.99770075,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"323"},{"span":{"begin":21216,"end":21232},"obj":"0.83079296,evidence,cleaner0,2023-07-05T10:43:12Z,DUMMY:","id":"324"},{"span":{"begin":21262,"end":21270},"obj":"0.9937124,complex_assembly,cleaner0,2023-07-05T10:38:43Z,GO:","id":"325"},{"span":{"begin":21285,"end":21305},"obj":"0.9262293,experimental_method,cleaner0,2023-07-05T12:16:54Z,MESH:","id":"326"},{"span":{"begin":21306,"end":21329},"obj":"0.9843981,evidence,cleaner0,2023-07-05T10:43:15Z,DUMMY:","id":"327"},{"span":{"begin":21360,"end":21363},"obj":"0.99798906,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"328"},{"span":{"begin":21364,"end":21392},"obj":"0.8665679,evidence,cleaner0,2023-07-05T10:43:17Z,DUMMY:","id":"329"},{"span":{"begin":21577,"end":21580},"obj":"0.9983839,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"330"},{"span":{"begin":21657,"end":21663},"obj":"0.88909703,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"331"},{"span":{"begin":21696,"end":21699},"obj":"0.9981768,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"332"},{"span":{"begin":21717,"end":21720},"obj":"0.9861231,residue_name,cleaner0,2023-07-05T12:07:24Z,SO:","id":"333"},{"span":{"begin":21725,"end":21728},"obj":"0.9858482,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"334"},{"span":{"begin":21844,"end":21847},"obj":"0.9861166,residue_name,cleaner0,2023-07-05T10:42:44Z,SO:","id":"335"},{"span":{"begin":21864,"end":21868},"obj":"0.97520036,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"336"},{"span":{"begin":21965,"end":21968},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"694"},{"span":{"begin":22063,"end":22067},"obj":"0.9912158,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"337"},{"span":{"begin":22068,"end":22072},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"824"},{"span":{"begin":22079,"end":22082},"obj":"0.989652,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"338"},{"span":{"begin":22091,"end":22094},"obj":"0.98959446,residue_name,cleaner0,2023-07-05T12:34:05Z,SO:","id":"339"},{"span":{"begin":22116,"end":22123},"obj":"0.9787446,oligomeric_state,cleaner0,2023-07-05T10:43:50Z,DUMMY:","id":"340"},{"span":{"begin":22235,"end":22238},"obj":"0.9698287,residue_name,cleaner0,2023-07-05T12:34:09Z,SO:","id":"341"},{"span":{"begin":22245,"end":22248},"obj":"0.95125747,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"342"},{"span":{"begin":22258,"end":22264},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T10:43:57Z","id":"799"},{"span":{"begin":22435,"end":22443},"obj":"0.9959565,protein_state,cleaner0,2023-07-05T10:44:09Z,DUMMY:","id":"344"},{"span":{"begin":22448,"end":22453},"obj":"0.9911316,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"345"},{"span":{"begin":22454,"end":22458},"obj":"0.99624735,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"346"},{"span":{"begin":22573,"end":22577},"obj":"0.8192733,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"347"},{"span":{"begin":22603,"end":22625},"obj":"0.99758184,site,cleaner0,2023-07-05T10:43:27Z,SO:","id":"348"},{"span":{"begin":22667,"end":22675},"obj":"0.9959115,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"349"},{"span":{"begin":22676,"end":22680},"obj":"0.99391973,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"350"},{"span":{"begin":22719,"end":22739},"obj":"0.9969743,site,cleaner0,2023-07-05T10:43:29Z,SO:","id":"351"},{"span":{"begin":22779,"end":22784},"obj":"0.9965004,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"352"},{"span":{"begin":22785,"end":22789},"obj":"0.9917121,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"353"},{"span":{"begin":22879,"end":22884},"obj":"0.99910825,residue_name_number,cleaner0,2023-07-05T10:44:41Z,DUMMY:","id":"354"},{"span":{"begin":22886,"end":22891},"obj":"0.99910176,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"355"},{"span":{"begin":22896,"end":22901},"obj":"0.99909663,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"356"},{"span":{"begin":22919,"end":22922},"obj":"0.9915868,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"357"},{"span":{"begin":22958,"end":22962},"obj":"0.7789828,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"358"},{"span":{"begin":22963,"end":22967},"obj":"0.4135374,structure_element,cleaner0,2023-07-05T11:58:12Z,SO:","id":"359"},{"span":{"begin":22968,"end":22976},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:54Z","id":"883"},{"span":{"begin":23003,"end":23018},"obj":"0.9754962,evidence,cleaner0,2023-07-05T12:21:41Z,DUMMY:","id":"360"},{"span":{"begin":23041,"end":23067},"obj":"0.9385281,experimental_method,cleaner0,2023-07-05T10:44:16Z,MESH:","id":"361"},{"span":{"begin":23101,"end":23117},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:17:44Z","id":"888"},{"span":{"begin":23180,"end":23193},"obj":"0.9535044,evidence,cleaner0,2023-07-05T12:21:49Z,DUMMY:","id":"363"},{"span":{"begin":23213,"end":23218},"obj":"0.99416935,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"364"},{"span":{"begin":23223,"end":23231},"obj":"0.98500234,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"365"},{"span":{"begin":23287,"end":23293},"obj":"0.95402676,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"366"},{"span":{"begin":23306,"end":23311},"obj":"0.9990717,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"367"},{"span":{"begin":23315,"end":23324},"obj":"0.99607676,protein_state,cleaner0,2023-07-05T12:32:01Z,DUMMY:","id":"368"},{"span":{"begin":23339,"end":23347},"obj":"0.9939761,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"369"},{"span":{"begin":23348,"end":23352},"obj":"0.94174945,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"370"},{"span":{"begin":23451,"end":23455},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:07:58Z","id":"741"},{"span":{"begin":23456,"end":23460},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"827"},{"span":{"begin":23461,"end":23468},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:42Z","id":"880"},{"span":{"begin":23474,"end":23479},"obj":"0.9990544,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"372"},{"span":{"begin":23567,"end":23569},"obj":"0.98224247,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"373"},{"span":{"begin":23570,"end":23573},"obj":"0.996082,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"374"},{"span":{"begin":23597,"end":23602},"obj":"0.99904436,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"375"},{"span":{"begin":23610,"end":23627},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:00:19Z","id":"833"},{"span":{"begin":23628,"end":23637},"obj":"0.9971259,evidence,cleaner0,2023-07-05T12:21:52Z,DUMMY:","id":"378"},{"span":{"begin":23692,"end":23694},"obj":"0.43124557,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"379"},{"span":{"begin":23722,"end":23741},"obj":"site,SO:,cleaner0,2023-07-05T10:45:21Z","id":"806"},{"span":{"begin":23751,"end":23756},"obj":"0.99898416,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"383"},{"span":{"begin":23760,"end":23762},"obj":"0.5508266,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"384"},{"span":{"begin":23790,"end":23797},"obj":"0.8253004,evidence,cleaner0,2023-07-05T12:21:57Z,DUMMY:","id":"385"},{"span":{"begin":23815,"end":23818},"obj":"0.59934,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"386"},{"span":{"begin":23855,"end":23860},"obj":"0.9990036,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"387"},{"span":{"begin":23870,"end":23875},"obj":"0.99900705,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"388"},{"span":{"begin":23913,"end":23916},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"697"},{"span":{"begin":24004,"end":24009},"obj":"0.9987974,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"390"},{"span":{"begin":24054,"end":24059},"obj":"0.9982838,chemical,cleaner0,2023-07-05T12:14:22Z,CHEBI:","id":"391"},{"span":{"begin":24072,"end":24095},"obj":"site,SO:,cleaner0,2023-07-05T10:45:45Z","id":"807"},{"span":{"begin":24167,"end":24172},"obj":"0.99884206,residue_name_number,cleaner0,2023-07-05T10:45:53Z,DUMMY:","id":"394"},{"span":{"begin":24289,"end":24298},"obj":"0.99792117,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:26:50Z,SO:","id":"395"},{"span":{"begin":24349,"end":24359},"obj":"0.99548495,protein_type,cleaner0,2023-07-05T12:27:28Z,MESH:","id":"396"},{"span":{"begin":24368,"end":24377},"obj":"0.996011,evidence,cleaner0,2023-07-05T12:22:00Z,DUMMY:","id":"397"},{"span":{"begin":24448,"end":24463},"obj":"0.98592824,evidence,cleaner0,2023-07-05T12:22:03Z,DUMMY:","id":"398"},{"span":{"begin":24472,"end":24480},"obj":"0.995103,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"399"},{"span":{"begin":24481,"end":24486},"obj":"0.98567003,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"400"},{"span":{"begin":24487,"end":24492},"obj":"0.9971819,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"401"},{"span":{"begin":24543,"end":24548},"obj":"0.99736005,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"402"},{"span":{"begin":24676,"end":24679},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"699"},{"span":{"begin":24701,"end":24706},"obj":"0.6723021,chemical,cleaner0,2023-07-05T12:14:46Z,CHEBI:","id":"404"},{"span":{"begin":24797,"end":24807},"obj":"0.99513197,protein_state,cleaner0,2023-07-05T12:32:17Z,DUMMY:","id":"405"},{"span":{"begin":24808,"end":24811},"obj":"0.97005063,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"406"},{"span":{"begin":24817,"end":24840},"obj":"0.99278337,evidence,cleaner0,2023-07-05T12:22:06Z,DUMMY:","id":"407"},{"span":{"begin":24886,"end":24891},"obj":"0.99656266,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"408"},{"span":{"begin":24896,"end":24904},"obj":"0.9923832,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"409"},{"span":{"begin":24905,"end":24909},"obj":"0.23798376,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"410"},{"span":{"begin":24919,"end":24924},"obj":"0.99764353,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"411"},{"span":{"begin":24982,"end":24985},"obj":"0.4976674,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"412"},{"span":{"begin":25064,"end":25069},"obj":"0.9930019,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"414"},{"span":{"begin":25119,"end":25122},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"700"},{"span":{"begin":25219,"end":25224},"obj":"0.99905163,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"416"},{"span":{"begin":25244,"end":25246},"obj":"0.9022129,residue_name_number,cleaner0,2023-07-05T10:52:10Z,DUMMY:","id":"417"},{"span":{"begin":25266,"end":25293},"obj":"site,SO:,cleaner0,2023-07-05T10:46:58Z","id":"808"},{"span":{"begin":25343,"end":25349},"obj":"0.9752722,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"421"},{"span":{"begin":25370,"end":25375},"obj":"0.999049,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"422"},{"span":{"begin":25418,"end":25421},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:21Z","id":"702"},{"span":{"begin":25443,"end":25448},"obj":"0.99901557,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"423"},{"span":{"begin":25531,"end":25536},"obj":"0.99905235,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"424"},{"span":{"begin":25578,"end":25583},"obj":"0.99905616,residue_name_number,cleaner0,2023-07-05T10:51:41Z,DUMMY:","id":"425"},{"span":{"begin":25621,"end":25623},"obj":"0.54564714,residue_name_number,cleaner0,2023-07-05T10:52:23Z,DUMMY:","id":"426"},{"span":{"begin":25679,"end":25700},"obj":"0.99768096,site,cleaner0,2023-07-05T12:04:01Z,SO:","id":"427"},{"span":{"begin":25706,"end":25712},"obj":"0.9751469,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"428"},{"span":{"begin":25717,"end":25722},"obj":"0.99891317,residue_name_number,cleaner0,2023-07-05T10:51:42Z,DUMMY:","id":"429"},{"span":{"begin":25782,"end":25784},"obj":"0.7176499,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"430"},{"span":{"begin":25818,"end":25823},"obj":"0.9988103,residue_name_number,cleaner0,2023-07-05T10:51:42Z,DUMMY:","id":"431"},{"span":{"begin":25850,"end":25855},"obj":"0.99893457,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"432"},{"span":{"begin":25860,"end":25865},"obj":"0.9989254,residue_name_number,cleaner0,2023-07-05T10:51:42Z,DUMMY:","id":"433"},{"span":{"begin":25946,"end":25948},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T10:28:30Z","id":"754"},{"span":{"begin":26012,"end":26020},"obj":"0.9915398,complex_assembly,cleaner0,2023-07-05T10:38:43Z,GO:","id":"434"},{"span":{"begin":26162,"end":26191},"obj":"0.9947875,evidence,cleaner0,2023-07-05T12:22:11Z,DUMMY:","id":"435"},{"span":{"begin":26236,"end":26242},"obj":"0.78213966,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"437"},{"span":{"begin":26362,"end":26364},"obj":"0.64419585,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"438"},{"span":{"begin":26539,"end":26591},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T10:54:22Z","id":"815"},{"span":{"begin":26645,"end":26652},"obj":"0.98756266,evidence,cleaner0,2023-07-05T12:22:22Z,DUMMY:","id":"441"},{"span":{"begin":26719,"end":26722},"obj":"0.9878491,chemical,cleaner0,2023-07-05T10:26:21Z,CHEBI:","id":"442"},{"span":{"begin":26782,"end":26791},"obj":"0.9950579,protein_state,cleaner0,2023-07-05T12:32:29Z,DUMMY:","id":"443"},{"span":{"begin":26796,"end":26804},"obj":"0.9650826,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"444"},{"span":{"begin":26805,"end":26809},"obj":"0.45595852,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"445"},{"span":{"begin":26839,"end":26841},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T10:28:30Z","id":"755"},{"span":{"begin":26866,"end":26869},"obj":"0.97414523,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"446"},{"span":{"begin":26905,"end":26924},"obj":"0.7477479,protein_state,cleaner0,2023-07-05T12:32:46Z,DUMMY:","id":"447"},{"span":{"begin":27044,"end":27061},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:17:38Z","id":"889"},{"span":{"begin":27069,"end":27079},"obj":"0.99410534,complex_assembly,cleaner0,2023-07-05T12:31:03Z,GO:","id":"449"},{"span":{"begin":27088,"end":27091},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"767"},{"span":{"begin":27181,"end":27216},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T10:54:03Z","id":"814"},{"span":{"begin":27265,"end":27268},"obj":"0.9961176,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"455"},{"span":{"begin":27299,"end":27317},"obj":"0.9903002,evidence,cleaner0,2023-07-05T12:22:26Z,DUMMY:","id":"456"},{"span":{"begin":27331,"end":27334},"obj":"0.99770594,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"457"},{"span":{"begin":27352,"end":27360},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:54Z","id":"884"},{"span":{"begin":27362,"end":27365},"obj":"0.9490286,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"458"},{"span":{"begin":27443,"end":27446},"obj":"0.98482555,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"459"},{"span":{"begin":27528,"end":27530},"obj":"0.6900701,residue_name_number,cleaner0,2023-07-05T10:53:16Z,DUMMY:","id":"460"},{"span":{"begin":27531,"end":27540},"obj":"0.5953651,chemical,cleaner0,2023-07-05T12:14:51Z,CHEBI:","id":"461"},{"span":{"begin":27569,"end":27575},"obj":"0.9657221,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"462"},{"span":{"begin":27601,"end":27603},"obj":"0.48627108,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"463"},{"span":{"begin":27605,"end":27607},"obj":"0.43101338,residue_name_number,cleaner0,2023-07-05T10:54:30Z,DUMMY:","id":"464"},{"span":{"begin":27612,"end":27614},"obj":"0.69601625,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"465"},{"span":{"begin":27646,"end":27648},"obj":"0.97514343,residue_name_number,cleaner0,2023-07-05T10:53:17Z,DUMMY:","id":"466"},{"span":{"begin":27740,"end":27744},"obj":"0.8990134,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"468"},{"span":{"begin":27753,"end":27758},"obj":"0.9884177,chemical,cleaner0,2023-07-05T12:15:01Z,CHEBI:","id":"469"},{"span":{"begin":27815,"end":27823},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:54Z","id":"885"},{"span":{"begin":27837,"end":27842},"obj":"0.99823785,residue_name_number,cleaner0,2023-07-05T10:45:53Z,DUMMY:","id":"470"},{"span":{"begin":27885,"end":27893},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:54Z","id":"886"},{"span":{"begin":27911,"end":27913},"obj":"0.9919527,residue_name_number,cleaner0,2023-07-05T10:53:17Z,DUMMY:","id":"471"},{"span":{"begin":27914,"end":27920},"obj":"0.7579533,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"472"},{"span":{"begin":28006,"end":28009},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:22Z","id":"706"},{"span":{"begin":28019,"end":28025},"obj":"0.66986865,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"473"},{"span":{"begin":28081,"end":28084},"obj":"0.9113056,residue_name,cleaner0,2023-07-05T10:42:44Z,SO:","id":"474"},{"span":{"begin":28264,"end":28267},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:22Z","id":"707"},{"span":{"begin":28295,"end":28312},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T10:53:41Z","id":"813"},{"span":{"begin":28414,"end":28417},"obj":"0.86929446,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"478"},{"span":{"begin":28527,"end":28530},"obj":"0.99296665,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"479"},{"span":{"begin":28548,"end":28552},"obj":"0.98447126,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"480"},{"span":{"begin":28646,"end":28651},"obj":"0.9987546,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"481"},{"span":{"begin":28656,"end":28661},"obj":"0.99878544,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"482"},{"span":{"begin":28679,"end":28682},"obj":"0.99426657,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"483"},{"span":{"begin":28719,"end":28726},"obj":"0.97147286,chemical,cleaner0,2023-07-05T12:15:09Z,CHEBI:","id":"484"},{"span":{"begin":28734,"end":28736},"obj":"0.92182314,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"485"},{"span":{"begin":28741,"end":28743},"obj":"0.95111024,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"486"},{"span":{"begin":28783,"end":28788},"obj":"0.998728,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"487"},{"span":{"begin":28790,"end":28795},"obj":"0.99873954,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"488"},{"span":{"begin":28835,"end":28843},"obj":"0.9912282,protein_state,cleaner0,2023-07-05T12:32:51Z,DUMMY:","id":"489"},{"span":{"begin":28844,"end":28847},"obj":"0.9868809,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"490"},{"span":{"begin":28900,"end":28943},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:18:19Z","id":"890"},{"span":{"begin":28993,"end":28995},"obj":"0.7989518,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"493"},{"span":{"begin":29024,"end":29028},"obj":"0.98919463,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"495"},{"span":{"begin":29047,"end":29049},"obj":"0.78089446,residue_name_number,cleaner0,2023-07-05T10:54:30Z,DUMMY:","id":"496"},{"span":{"begin":29054,"end":29056},"obj":"0.8507618,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"497"},{"span":{"begin":29092,"end":29112},"obj":"0.98744667,evidence,cleaner0,2023-07-05T12:22:33Z,DUMMY:","id":"498"},{"span":{"begin":29116,"end":29120},"obj":"0.99020547,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"499"},{"span":{"begin":29122,"end":29125},"obj":"0.99115556,evidence,cleaner0,2023-07-05T12:22:36Z,DUMMY:","id":"500"},{"span":{"begin":29147,"end":29152},"obj":"0.99872905,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"501"},{"span":{"begin":29157,"end":29162},"obj":"0.998755,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"502"},{"span":{"begin":29253,"end":29259},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T10:43:57Z","id":"802"},{"span":{"begin":29261,"end":29271},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:23:06Z","id":"895"},{"span":{"begin":29389,"end":29394},"obj":"0.9987036,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"504"},{"span":{"begin":29419,"end":29428},"obj":"0.9961844,protein_state,cleaner0,2023-07-05T12:32:54Z,DUMMY:","id":"505"},{"span":{"begin":29429,"end":29433},"obj":"0.9805304,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"506"},{"span":{"begin":29439,"end":29444},"obj":"0.9988978,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"507"},{"span":{"begin":29506,"end":29511},"obj":"0.9990214,residue_name_number,cleaner0,2023-07-05T10:55:21Z,DUMMY:","id":"508"},{"span":{"begin":29516,"end":29521},"obj":"0.99905556,residue_name_number,cleaner0,2023-07-05T10:55:26Z,DUMMY:","id":"509"},{"span":{"begin":29556,"end":29565},"obj":"0.95854217,protein_state,cleaner0,2023-07-05T12:32:59Z,DUMMY:","id":"510"},{"span":{"begin":29582,"end":29584},"obj":"0.996298,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"511"},{"span":{"begin":29666,"end":29671},"obj":"0.9989222,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"512"},{"span":{"begin":29675,"end":29684},"obj":"0.9960868,protein_state,cleaner0,2023-07-05T12:33:02Z,DUMMY:","id":"513"},{"span":{"begin":29685,"end":29689},"obj":"0.9864499,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"514"},{"span":{"begin":30039,"end":30047},"obj":"0.9948141,protein_state,cleaner0,2023-07-05T12:33:06Z,DUMMY:","id":"515"},{"span":{"begin":30048,"end":30051},"obj":"0.99623907,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"516"},{"span":{"begin":30096,"end":30101},"obj":"0.99894124,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"517"},{"span":{"begin":30196,"end":30201},"obj":"0.9985372,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"518"},{"span":{"begin":30242,"end":30264},"obj":"0.76363486,evidence,cleaner0,2023-07-05T12:23:16Z,DUMMY:","id":"519"},{"span":{"begin":30345,"end":30350},"obj":"0.9988926,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"520"},{"span":{"begin":30440,"end":30444},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:07:58Z","id":"745"},{"span":{"begin":30450,"end":30482},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:23:39Z","id":"896"},{"span":{"begin":30552,"end":30563},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:04:50Z","id":"838"},{"span":{"begin":30586,"end":30591},"obj":"0.99887615,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"523"},{"span":{"begin":30592,"end":30605},"obj":"0.97079873,site,cleaner0,2023-07-05T12:34:26Z,SO:","id":"524"},{"span":{"begin":30625,"end":30628},"obj":"0.8287284,residue_name,cleaner0,2023-07-05T12:34:16Z,SO:","id":"525"},{"span":{"begin":30652,"end":30655},"obj":"0.9915752,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"526"},{"span":{"begin":30669,"end":30674},"obj":"0.998931,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"527"},{"span":{"begin":30774,"end":30777},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T12:23:52Z","id":"897"},{"span":{"begin":30788,"end":30796},"obj":"0.59207654,evidence,cleaner0,2023-07-05T12:23:58Z,DUMMY:","id":"528"},{"span":{"begin":31112,"end":31119},"obj":"0.99064636,evidence,cleaner0,2023-07-05T12:24:02Z,DUMMY:","id":"530"},{"span":{"begin":31543,"end":31547},"obj":"0.86443084,protein_state,cleaner0,2023-07-05T12:33:09Z,DUMMY:","id":"533"},{"span":{"begin":31552,"end":31559},"obj":"0.7418846,protein_state,cleaner0,2023-07-05T12:33:11Z,DUMMY:","id":"534"},{"span":{"begin":31560,"end":31563},"obj":"0.9973688,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"535"},{"span":{"begin":31991,"end":32013},"obj":"0.99785984,site,cleaner0,2023-07-05T12:34:37Z,SO:","id":"537"},{"span":{"begin":32015,"end":32018},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:22Z","id":"712"},{"span":{"begin":32076,"end":32081},"obj":"0.999079,residue_name_number,cleaner0,2023-07-05T10:56:05Z,DUMMY:","id":"538"},{"span":{"begin":32083,"end":32088},"obj":"0.99905926,residue_name_number,cleaner0,2023-07-05T10:56:10Z,DUMMY:","id":"539"},{"span":{"begin":32093,"end":32098},"obj":"0.9990657,residue_name_number,cleaner0,2023-07-05T10:56:14Z,DUMMY:","id":"540"},{"span":{"begin":32154,"end":32158},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:07:58Z","id":"746"},{"span":{"begin":32159,"end":32164},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:05:25Z","id":"843"},{"span":{"begin":32268,"end":32273},"obj":"0.9930227,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"542"},{"span":{"begin":32278,"end":32286},"obj":"0.9660058,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"543"},{"span":{"begin":32287,"end":32291},"obj":"0.9864768,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"544"},{"span":{"begin":32328,"end":32332},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:07:58Z","id":"747"},{"span":{"begin":32333,"end":32337},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"828"},{"span":{"begin":32355,"end":32360},"obj":"0.9962069,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"546"},{"span":{"begin":32361,"end":32365},"obj":"0.9905319,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"547"},{"span":{"begin":32367,"end":32372},"obj":"0.9990728,residue_name_number,cleaner0,2023-07-05T10:56:14Z,DUMMY:","id":"548"},{"span":{"begin":32400,"end":32406},"obj":"0.99010086,residue_name,cleaner0,2023-07-05T10:56:37Z,SO:","id":"549"},{"span":{"begin":32425,"end":32433},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:54Z","id":"881"},{"span":{"begin":32446,"end":32454},"obj":"0.9937517,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"550"},{"span":{"begin":32455,"end":32459},"obj":"0.9874014,complex_assembly,cleaner0,2023-07-05T12:07:58Z,GO:","id":"551"},{"span":{"begin":32491,"end":32496},"obj":"0.999064,residue_name_number,cleaner0,2023-07-05T10:56:14Z,DUMMY:","id":"552"},{"span":{"begin":32541,"end":32547},"obj":"0.9762691,chemical,cleaner0,2023-07-05T12:15:18Z,CHEBI:","id":"553"},{"span":{"begin":32556,"end":32563},"obj":"structure_element,SO:,cleaner0,2023-07-05T12:15:42Z","id":"879"},{"span":{"begin":32756,"end":32774},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T12:18:42Z","id":"891"},{"span":{"begin":33054,"end":33056},"obj":"0.74215937,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"555"},{"span":{"begin":33080,"end":33083},"obj":"0.95398015,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"556"},{"span":{"begin":33095,"end":33099},"obj":"0.9726016,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"557"},{"span":{"begin":33153,"end":33157},"obj":"0.8587137,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"558"},{"span":{"begin":33186,"end":33191},"obj":"0.9990075,residue_name_number,cleaner0,2023-07-05T10:51:42Z,DUMMY:","id":"559"},{"span":{"begin":33196,"end":33201},"obj":"0.99903595,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"560"},{"span":{"begin":33227,"end":33229},"obj":"0.65299237,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"561"},{"span":{"begin":33234,"end":33236},"obj":"0.5014381,residue_name_number,cleaner0,2023-07-05T10:52:11Z,DUMMY:","id":"562"},{"span":{"begin":33304,"end":33307},"obj":"0.98193204,residue_name,cleaner0,2023-07-05T10:56:31Z,SO:","id":"563"},{"span":{"begin":33530,"end":33534},"obj":"0.9829249,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"565"},{"span":{"begin":33536,"end":33542},"obj":"0.6355414,evidence,cleaner0,2023-07-05T10:43:57Z,DUMMY:","id":"566"},{"span":{"begin":33584,"end":33587},"obj":"0.97448653,residue_name,cleaner0,2023-07-05T10:56:34Z,SO:","id":"567"},{"span":{"begin":33609,"end":33613},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"829"},{"span":{"begin":33642,"end":33646},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"830"},{"span":{"begin":33725,"end":33749},"obj":"0.9927671,evidence,cleaner0,2023-07-05T12:24:08Z,DUMMY:","id":"568"},{"span":{"begin":33771,"end":33774},"obj":"0.56909597,evidence,cleaner0,2023-07-05T12:24:17Z,DUMMY:","id":"569"},{"span":{"begin":33806,"end":33809},"obj":"0.9574091,residue_name,cleaner0,2023-07-05T10:56:40Z,SO:","id":"570"},{"span":{"begin":33841,"end":33844},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:26:22Z","id":"713"},{"span":{"begin":33940,"end":33962},"obj":"0.99812096,site,cleaner0,2023-07-05T12:34:42Z,SO:","id":"571"},{"span":{"begin":33974,"end":33978},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:07:59Z","id":"748"},{"span":{"begin":33979,"end":33983},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"831"},{"span":{"begin":33998,"end":34003},"obj":"0.9991387,residue_name_number,cleaner0,2023-07-05T12:00:25Z,DUMMY:","id":"573"},{"span":{"begin":34031,"end":34033},"obj":"0.48927557,residue_name_number,cleaner0,2023-07-05T10:52:24Z,DUMMY:","id":"574"},{"span":{"begin":34052,"end":34074},"obj":"0.9979715,site,cleaner0,2023-07-05T12:34:45Z,SO:","id":"575"},{"span":{"begin":34112,"end":34130},"obj":"0.9856348,evidence,cleaner0,2023-07-05T12:24:21Z,DUMMY:","id":"576"},{"span":{"begin":34139,"end":34148},"obj":"0.99598575,protein_state,cleaner0,2023-07-05T12:33:16Z,DUMMY:","id":"577"},{"span":{"begin":34153,"end":34161},"obj":"0.9913564,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"578"},{"span":{"begin":34162,"end":34166},"obj":"0.9880157,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"579"},{"span":{"begin":34392,"end":34403},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:06:23Z","id":"874"},{"span":{"begin":34408,"end":34419},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:06:42Z","id":"876"},{"span":{"begin":34486,"end":34495},"obj":"0.99518895,protein_state,cleaner0,2023-07-05T12:33:22Z,DUMMY:","id":"582"},{"span":{"begin":34596,"end":34598},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T10:28:30Z","id":"756"},{"span":{"begin":34693,"end":34708},"obj":"0.9768747,protein_type,cleaner0,2023-07-05T12:27:33Z,MESH:","id":"584"},{"span":{"begin":34717,"end":34739},"obj":"0.992797,site,cleaner0,2023-07-05T12:35:08Z,SO:","id":"585"},{"span":{"begin":34956,"end":34959},"obj":"0.98401004,chemical,cleaner0,2023-07-05T10:36:34Z,CHEBI:","id":"587"},{"span":{"begin":34964,"end":34967},"obj":"0.98465955,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"588"},{"span":{"begin":35124,"end":35127},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"772"},{"span":{"begin":35152,"end":35181},"obj":"0.99563825,site,cleaner0,2023-07-05T12:35:12Z,SO:","id":"589"},{"span":{"begin":35299,"end":35302},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"774"},{"span":{"begin":35369,"end":35371},"obj":"0.62370133,experimental_method,cleaner0,2023-07-05T10:28:30Z,MESH:","id":"591"},{"span":{"begin":35487,"end":35498},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T12:04:56Z","id":"842"},{"span":{"begin":35606,"end":35619},"obj":"0.53609496,complex_assembly,cleaner0,2023-07-05T12:13:58Z,GO:","id":"593"},{"span":{"begin":35760,"end":35780},"obj":"0.9972315,site,cleaner0,2023-07-05T12:34:49Z,SO:","id":"594"},{"span":{"begin":35875,"end":35880},"obj":"protein_state,DUMMY:,cleaner0,2023-07-05T10:43:39Z","id":"794"},{"span":{"begin":35900,"end":35903},"obj":"0.9973586,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"595"},{"span":{"begin":35984,"end":35992},"obj":"0.98719054,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"596"},{"span":{"begin":35993,"end":35997},"obj":"0.6919731,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"597"},{"span":{"begin":36055,"end":36077},"obj":"0.9982071,site,cleaner0,2023-07-05T12:34:52Z,SO:","id":"599"},{"span":{"begin":36079,"end":36084},"obj":"0.9990889,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"600"},{"span":{"begin":36086,"end":36091},"obj":"0.99907863,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"601"},{"span":{"begin":36093,"end":36098},"obj":"0.9990723,residue_name_number,cleaner0,2023-07-05T10:44:50Z,DUMMY:","id":"602"},{"span":{"begin":36317,"end":36321},"obj":"0.87554866,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"603"},{"span":{"begin":36331,"end":36334},"obj":"0.99667054,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"604"},{"span":{"begin":36452,"end":36455},"obj":"0.9962542,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"605"},{"span":{"begin":36513,"end":36516},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T10:36:34Z","id":"775"},{"span":{"begin":41496,"end":41513},"obj":"complex_assembly,GO:,cleaner0,2023-07-05T10:58:32Z","id":"817"},{"span":{"begin":41579,"end":41584},"obj":"0.99105424,protein_state,cleaner0,2023-07-05T10:43:39Z,DUMMY:","id":"609"},{"span":{"begin":41585,"end":41595},"obj":"0.9840899,chemical,cleaner0,2023-07-05T12:16:01Z,CHEBI:","id":"610"},{"span":{"begin":41641,"end":41644},"obj":"0.9981456,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"611"},{"span":{"begin":41715,"end":41721},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:12:10Z","id":"877"},{"span":{"begin":41729,"end":41737},"obj":"0.9932771,complex_assembly,cleaner0,2023-07-05T10:38:44Z,GO:","id":"615"},{"span":{"begin":41746,"end":41753},"obj":"0.9954058,evidence,cleaner0,2023-07-05T12:24:38Z,DUMMY:","id":"616"},{"span":{"begin":41835,"end":41851},"obj":"0.7991534,evidence,cleaner0,2023-07-05T12:24:42Z,DUMMY:","id":"617"},{"span":{"begin":41873,"end":41881},"obj":"0.99266356,complex_assembly,cleaner0,2023-07-05T10:38:44Z,GO:","id":"618"},{"span":{"begin":41882,"end":41891},"obj":"0.98201466,evidence,cleaner0,2023-07-05T12:24:45Z,DUMMY:","id":"619"},{"span":{"begin":41906,"end":41920},"obj":"0.9719779,evidence,cleaner0,2023-07-05T12:24:49Z,DUMMY:","id":"620"},{"span":{"begin":41922,"end":41945},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:25:15Z","id":"898"},{"span":{"begin":42115,"end":42129},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:13:13Z","id":"878"},{"span":{"begin":42183,"end":42186},"obj":"0.96845776,evidence,cleaner0,2023-07-05T12:25:20Z,DUMMY:","id":"626"},{"span":{"begin":42188,"end":42213},"obj":"0.98903877,evidence,cleaner0,2023-07-05T12:25:23Z,DUMMY:","id":"627"},{"span":{"begin":42313,"end":42317},"obj":"0.5221266,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"628"},{"span":{"begin":42350,"end":42364},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:25:43Z","id":"899"},{"span":{"begin":42392,"end":42396},"obj":"0.7290474,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"630"},{"span":{"begin":42460,"end":42507},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T12:26:14Z","id":"900"},{"span":{"begin":42630,"end":42648},"obj":"0.9945644,evidence,cleaner0,2023-07-05T12:26:18Z,DUMMY:","id":"638"},{"span":{"begin":42672,"end":42677},"obj":"0.9991478,residue_name_number,cleaner0,2023-07-05T10:44:51Z,DUMMY:","id":"639"},{"span":{"begin":42721,"end":42747},"obj":"0.8718893,evidence,cleaner0,2023-07-05T12:26:29Z,DUMMY:","id":"641"},{"span":{"begin":42896,"end":42899},"obj":"0.997905,chemical,cleaner0,2023-07-05T10:26:22Z,CHEBI:","id":"643"},{"span":{"begin":42900,"end":42907},"obj":"0.9303295,evidence,cleaner0,2023-07-05T12:26:36Z,DUMMY:","id":"644"},{"span":{"begin":42939,"end":42945},"obj":"0.89408696,evidence,cleaner0,2023-07-05T12:26:41Z,DUMMY:","id":"645"},{"span":{"begin":42991,"end":42994},"obj":"0.9847978,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:26:50Z,SO:","id":"646"},{"span":{"begin":43002,"end":43005},"obj":"0.97973424,residue_name,cleaner0,2023-07-05T10:42:19Z,SO:","id":"647"},{"span":{"begin":43026,"end":43034},"obj":"0.9919364,complex_assembly,cleaner0,2023-07-05T10:38:44Z,GO:","id":"648"},{"span":{"begin":43137,"end":43142},"obj":"0.98781407,protein_state,cleaner0,2023-07-05T10:43:40Z,DUMMY:","id":"649"},{"span":{"begin":43147,"end":43155},"obj":"0.94484127,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"650"},{"span":{"begin":43248,"end":43252},"obj":"0.72071564,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"651"},{"span":{"begin":43253,"end":43257},"obj":"structure_element,SO:,cleaner0,2023-07-05T11:58:12Z","id":"832"},{"span":{"begin":43289,"end":43295},"obj":"0.93198663,evidence,cleaner0,2023-07-05T12:26:44Z,DUMMY:","id":"652"},{"span":{"begin":43398,"end":43404},"obj":"0.7863771,evidence,cleaner0,2023-07-05T12:26:53Z,DUMMY:","id":"653"},{"span":{"begin":43426,"end":43431},"obj":"0.99909854,residue_name_number,cleaner0,2023-07-05T10:44:42Z,DUMMY:","id":"655"},{"span":{"begin":43440,"end":43445},"obj":"0.9990896,residue_name_number,cleaner0,2023-07-05T10:44:46Z,DUMMY:","id":"656"},{"span":{"begin":43454,"end":43459},"obj":"0.9990759,residue_name_number,cleaner0,2023-07-05T10:44:51Z,DUMMY:","id":"657"},{"span":{"begin":43469,"end":43474},"obj":"0.9990729,residue_name_number,cleaner0,2023-07-05T10:44:51Z,DUMMY:","id":"658"},{"span":{"begin":43484,"end":43489},"obj":"0.9990627,residue_name_number,cleaner0,2023-07-05T10:51:36Z,DUMMY:","id":"659"},{"span":{"begin":43501,"end":43506},"obj":"0.9990792,residue_name_number,cleaner0,2023-07-05T10:51:42Z,DUMMY:","id":"660"},{"span":{"begin":43584,"end":43589},"obj":"0.9931265,protein_state,cleaner0,2023-07-05T10:43:40Z,DUMMY:","id":"661"},{"span":{"begin":43590,"end":43598},"obj":"0.9739872,protein_state,cleaner0,2023-07-05T10:44:10Z,DUMMY:","id":"662"},{"span":{"begin":43600,"end":43621},"obj":"0.9972383,site,cleaner0,2023-07-05T12:34:57Z,SO:","id":"663"},{"span":{"begin":43649,"end":43653},"obj":"0.95457613,complex_assembly,cleaner0,2023-07-05T12:07:59Z,GO:","id":"664"},{"span":{"begin":43672,"end":43718},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T10:59:56Z","id":"818"}],"relations":[]}]

annotated_BioC_JSON/PMC4871749_ann.json

@@ -0,0 +1 @@
+[{"sourceid":"4871749","sourcedb":"","project":"","target":"","text":"The Taf14 YEATS domain is a reader of histone crotonylation The discovery of new histone modifications is unfolding at startling rates, however, the identification of effectors capable of interpreting these modifications has lagged behind. Here we report the YEATS domain as an effective reader of histone lysine crotonylation – an epigenetic signature associated with active transcription. We show that the Taf14 YEATS domain engages crotonyllysine via a unique π-π-π-stacking mechanism and that other YEATS domains have crotonyllysine binding activity. Crotonylation of lysine residues (crotonyllysine, Kcr) has emerged as one of the fundamental histone post-translational modifications (PTMs) found in mammalian chromatin. This epigenetic PTM is widespread and enriched at active gene promoters and potentially enhancers. The crotonyllysine mark on histone H3K18 is produced by p300, a histone acetyltransferase also responsible for acetylation of histones. Owing to some differences in their genomic distribution, the crotonyllysine and acetyllysine (Kac) modifications have been linked to distinct functional outcomes. p300-catalyzed histone crotonylation, which is likely metabolically regulated, stimulates transcription to a greater degree than p300-catalyzed acetylation. The discovery of individual biological roles for the crotonyllysine and acetyllysine marks suggests that these PTMs can be read by distinct readers. While a number of acetyllysine readers have been identified and characterized, a specific reader of the crotonyllysine mark remains unknown (reviewed in). A recent survey of bromodomains (BDs) demonstrates that only one BD associates very weakly with a crotonylated peptide, however it binds more tightly to acetylated peptides, inferring that bromodomains do not possess physiologically relevant crotonyllysine binding activity. The family of acetyllysine readers has been expanded with the discovery that the YEATS (Yaf9, ENL, AF9, Taf14, Sas5) domains of human AF9 and yeast Taf14 are capable of recognizing the histone mark H3K9ac. The acetyllysine binding function of the AF9 YEATS domain is essential for the recruitment of the histone methyltransferase DOT1L to H3K9ac-containing chromatin and for DOT1L-mediated H3K79 methylation and transcription. Similarly, activation of a subset of genes and DNA damage repair in yeast require the acetyllysine binding activity of the Taf14 YEATS domain. Consistent with its role in gene regulation, Taf14 was identified as a core component of the transcription factor complexes TFIID and TFIIF. However, Taf14 is also found in a number of chromatin-remodeling complexes (i.e., INO80, SWI/SNF and RSC) and the histone acetyltransferase complex NuA3, indicating a multifaceted role of Taf14 in transcriptional regulation and chromatin biology. In this study, we identified the Taf14 YEATS domain as a reader of crotonyllysine that binds to histone H3 crotonylated at lysine 9 (H3K9cr) via a distinctive binding mechanism. We found that H3K9cr is present in yeast and is dynamically regulated. To elucidate the molecular basis for recognition of the H3K9cr mark, we obtained a crystal structure of the Taf14 YEATS domain in complex with H3K9cr5-13 (residues 5–13 of H3) peptide (Fig. 1, Supplementary Results, Supplementary Fig. 1 and Supplementary Table 1). The Taf14 YEATS domain adopts an immunoglobin-like β sandwich fold containing eight anti-parallel β strands linked by short loops that form a binding site for H3K9cr (Fig. 1b). The H3K9cr peptide lays in an extended conformation in an orientation orthogonal to the β strands and is stabilized through an extensive network of direct and water-mediated hydrogen bonds and a salt bridge (Fig. 1c). The most striking feature of the crotonyllysine recognition mechanism is the unique coordination of crotonylated lysine residue. The fully extended side chain of K9cr transverses the narrow tunnel, crossing the β sandwich at right angle in a corkscrew-like manner (Fig. 1b and Supplementary Figure 1b). The planar crotonyl group is inserted between Trp81 and Phe62 of the protein, the aromatic rings of which are positioned strictly parallel to each other and at equal distance from the crotonyl group, yielding a novel aromatic-amide/aliphatic-aromatic π-π-π-stacking system that, to our knowledge, has not been reported previously for any protein-protein interaction (Fig. 1d and Supplementary Fig. 1c). The side chain of Trp81 appears to adopt two conformations, one of which provides maximum π-stacking with the alkene functional group while the other rotamer affords maximum π-stacking with the amide π electrons (Supplementary Fig. 1c). The dual conformation of Trp81 is likely due to the conjugated nature of the C=C and C=O π-orbitals within the crotonyl functional group. In addition to π-π-π stacking, the crotonyl group is stabilized by a set of hydrogen bonds and electrostatic interactions. The π bond conjugation of the crotonyl group gives rise to a dipole moment of the alkene moiety, resulting in a partial positive charge on the β-carbon (Cβ) and a partial negative charge on the α-carbon (Cα). This provides the capability for the alkene moiety to form electrostatic contacts, as Cα and Cβ lay within electrostatic interaction distances of the carbonyl oxygen of Gln79 and of the hydroxyl group of Thr61, respectively. The hydroxyl group of Thr61 also participates in a hydrogen bond with the amide nitrogen of the K9cr side chain (Fig. 1d). The fixed position of the Thr61 hydroxyl group, which facilitates interactions with both the amide and Cα of K9cr, is achieved through a hydrogen bond with imidazole ring of His59. Extra stabilization of K9cr is attained by a hydrogen bond formed between its carbonyl oxygen and the backbone nitrogen of Trp81, as well as a water-mediated hydrogen bond with the backbone carbonyl group of Gly82 (Fig 1d). This distinctive mechanism was corroborated through mapping the Taf14 YEATS-H3K9cr binding interface in solution using NMR chemical shift perturbation analysis (Supplementary Fig. 2a, b). Binding of the Taf14 YEATS domain to H3K9cr is robust. The dissociation constant (Kd) for the Taf14 YEATS-H3K9cr5-13 complex was found to be 9.5 μM, as measured by fluorescence spectroscopy (Supplementary Fig. 2c). This value is in the range of binding affinities exhibited by the majority of histone readers, thus attesting to the physiological relevance of the H3K9cr recognition by Taf14. To determine whether H3K9cr is present in yeast, we generated whole cell extracts from logarithmically growing yeast cells and subjected them to Western blot analysis using antibodies directed towards H3K9cr, H3K9ac and H3 (Fig. 2a, b, Supplementary Fig. 3 and Supplementary Table 2). Both H3K9cr and H3K9ac were detected in yeast histones; to our knowledge, this is the first report of H3K9cr occurring in yeast. We next asked if H3K9cr is regulated by the actions of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Towards this end, we probed extracts derived from yeast cells in which major yeast HATs (HAT1, Gcn5, and Rtt109) or HDACs (Rpd3, Hos1, and Hos2) were deleted. As shown in Figure 2a, b and Supplementary Fig. 3e, H3K9cr levels were abolished or reduced considerably in the HAT deletion strains, whereas they were dramatically increased in the HDAC deletion strains. Furthermore, fluctuations in the H3K9cr levels were more substantial than fluctuations in the corresponding H3K9ac levels. Together, these results reveal that H3K9cr is a dynamic mark of chromatin in yeast and suggest an important role for this modification in transcription as it is regulated by HATs and HDACs. We have previously shown that among acetylated histone marks, the Taf14 YEATS domain prefers acetylated H3K9 (also see Supplementary Fig. 3b), however it binds to H3K9cr tighter. The selectivity of Taf14 towards crotonyllysine was substantiated by 1H,15N HSQC experiments, in which either H3K9cr5-13 or H3K9ac5-13 peptide was titrated into the 15N-labeled Taf14 YEATS domain (Fig. 2c and Supplementary Fig. 4a, b). Binding of H3K9cr induced resonance changes in slow exchange regime on the NMR time scale, indicative of strong interaction. In contrast, binding of H3K9ac resulted in an intermediate exchange, which is characteristic of a weaker association. Furthermore, crosspeaks of Gly80 and Trp81 of the YEATS domain were uniquely perturbed by H3K9cr and H3K9ac, indicating a different chemical environment in the respective crotonyllysine and acetyllysine binding pockets (Supplementary Fig. 4a). These differences support our model that Trp81 adopts two conformations upon complex formation with the H3K9cr mark as compared to H3K9ac (Supplementary Figs. 1c, d and 4c). One of the conformations, characterized by the π stacking involving two aromatic residues and the alkene group, is observed only in the YEATS-H3K9cr complex. To establish whether the Taf14 YEATS domain is able to recognize other recently identified acyllysine marks, we performed solution pull-down assays using H3 peptides acetylated, propionylated, butyrylated, and crotonylated at lysine 9 (residues 1–20 of H3). As shown in Figure 2d and Supplementary Fig. 5a, the Taf14 YEATS domain binds more strongly to H3K9cr1-20, as compared to other acylated histone peptides. The preference for H3K9cr over H3K9ac, H3K9pr and H3K9bu was supported by 1H,15N HSQC titration experiments. Addition of H3K9ac1-20, H3K9pr1-20, and H3K9bu1-20 peptides caused chemical shift perturbations in the Taf14 YEATS domain in intermediate exchange regime, implying that these interactions are weaker compared to the interaction with the H3K9cr1-20 peptide (Supplementary Fig. 5b). We concluded that H3K9cr is the preferred target of this domain. From comparative structural analysis of the YEATS complexes, Gly80 emerged as candidate residue potentially responsible for the preference for crotonyllysine. In attempt to generate a mutant capable of accommodating a short acetyl moiety but discriminating against a longer, planar crotonyl moiety, we mutated Gly80 to more bulky residues, however all mutants of Gly80 lost their binding activities towards either acylated peptide, suggesting that Gly80 is absolutely required for the interaction. In contrast, mutation of Val24, a residue located on another side of Trp81, had no effect on binding (Fig. 2d and Supplementary Fig. 5a, c). To determine if the binding to crotonyllysine is conserved, we tested human YEATS domains by pull-down experiments using singly and multiply acetylated, propionylated, butyrylated, and crotonylated histone peptides (Supplementary Fig. 6). We found that all YEATS domains tested are capable of binding to crotonyllysine peptides, though they display variable preferences for the acyl moieties. While YEATS2 and ENL showed selectivity for the crotonylated peptides, GAS41 and AF9 bound acylated peptides almost equally well. Unlike the YEATS domain, a known acetyllysine reader, bromodomain, does not recognize crotonyllysine. We assayed a large set of BDs in pull-down experiments and found that this module is highly specific for acetyllysine and propionyllysine containing peptides (Supplementary Fig. 7). However, bromodomains did not interact (or associated very weakly) with longer acyl modifications, including crotonyllysine, as in the case of BDs of TAF1 and BRD2, supporting recent reports. These results demonstrate that the YEATS domain is currently the sole reader of crotonyllysine. In conclusion, we have identified the YEATS domain of Taf14 as the first reader of histone crotonylation. The unique and previously unobserved aromatic-amide/aliphatic-aromatic π-π-π-stacking mechanism facilitates the specific recognition of the crotonyl moiety. We further demonstrate that H3K9cr exists in yeast and is dynamically regulated by HATs and HDACs. As we previously showed the importance of acyllysine binding by the Taf14 YEATS domain for the DNA damage response and gene transcription, it will be essential in the future to define the physiological role of crotonyllysine recognition and to differentiate the activities of Taf14 that are due to binding to crotonyllysine and acetyllysine modifications. Furthermore, the functional significance of crotonyllysine recognition by other YEATS proteins will be of great importance to elucidate and compare. ONLINE METHODS Protein expression and purification The Taf14 YEATS constructs (residues 1–132 or 1–137) were expressed in E. coli BL21 (DE3) RIL in either Luria Broth or M19 minimal media supplemented with 15NH4Cl and purified as N-terminal GST fusion proteins. Cells were harvested by centrifugation and resuspended in 50 mM HEPES (pH 7.5) supplemented with 150 mM NaCl and 1 mM TCEP. Cells are lysed by freeze-thaw followed by sonication. Proteins were purified on glutathione Sepharose 4B beads and the GST tag was cleaved with PreScission protease. X-ray data collection and structure determination Taf14 YEATS (residues 1–137) was concentrated to 9 mg/mL in 25 mM MES (pH 6.5) and incubated with 2 molar equivalence of the H3K9cr5-13 at RT for 30 mins prior to crystallization. Crystals were obtain via sitting drop diffusion method at 18°C by mixing 800 nL of protein/peptide solution with 800 nL of well solution composed of 44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0). X-ray diffraction data was collected at a wavelength of 1.54 Å at 100 K from a single crystal on the UC Denver Biophysical Core home source composed of a Rigaku Micromax 007 high frequency microfocus X-ray generator with a Pilatus 200K 2D area detector. HKL3000 was used for indexing, scaling, and data reduction. Solution was solved via molecular replacement with Phaser using the Taf14 YEATS domain (PDB 5D7E) as search model with waters, ligands, and peptide removed. Phenix was used for refinement of structure and waters were manually placed by inception of difference maps in Coot. Ramachandran plot indicates good stereochemistry of the three-dimensional structure with 100% of all residues falling within the favored (98%) and allowed (2%) regions. The crystallographic statistics are shown in Supplementary Table 1. NMR spectroscopy NMR spectroscopy was carried out on a Varian INOVA 600 MHz spectrometer outfitted with a cryogenic probe. Chemical shift perturbation (CSP) analysis was performed using uniformly 15N-labeled Taf14 (1–132). 1H,15N heteronuclear single quantum coherence (HSQC) spectra of the Taf14 YEATS domain were collected in the presence of increasing concentrations of either H3K9cr5-13, H3K9ac5-13, H3K9cr1-20, H3K9ac1-20 H3K9pr1-20, H3K9bu1-20 or free Kcr in PBS buffer pH 6.8, 8% D2O. Fluorescence binding assays Tryptophan fluorescence measurements were performed on a Fluorolog spectrofluorometer at room temperature as described. The samples containing 2 μM of Taf14 YEATS in PBS (pH 7.4) and increasing concentrations of H3K9cr5-13 were excited at 295 nm. Emission spectra were recorded from 310 to 340 nm with a 1 nm step size and a 0.5 sec integration time. The Kd value was determined using a nonlinear least-squares analysis and the equation:   where [L] is the concentration of the peptide, [P] is the concentration of the protein, ΔI is the observed change of signal intensity, and ΔImax is the difference in signal intensity of the free and bound states. The Kd values were averaged over 3 separate experiments, with error calculated as the standard deviation (SD). Peptide pull-downs YEATS domains in pGEX vectors were expressed in SoluBL21 cells (Amsbio) by induction with 1 mM IPTG at 16–18°C overnight with shaking. Cells were lysed by freeze-thaw and sonication then purified over glutathione agarose (Pierce) in a buffer containing 50 mM Tris pH 8.0, 500 mM NaCl, 20% glycerol (v/v) and 1 mM dithiothreitol (DTT). Peptide pull-downs were performed essentially as described except that the assay buffer contained 50 mM Tris pH 8.0, 500 mM NaCl, and 0.1% NP-40, and 500 pmols of biotinylated histone peptides were loaded onto streptavidin coated magnetic beads before incubation with 40 pmols of protein. Bound proteins were detected with rabbit GST antibody (Sigma, G7781). Point mutants were generated by site-directed mutagenesis and purified/assayed as described above. The YEATS domains of Taf14, AF9, ENL, and GAS41 were previously described. Western blotting Yeast cultures were grown in YPD media at 30°C to mid-log phase and extracts were prepared as previously described. Proteins from cell lysates were separated by SDS-PAGE and transferred to a PVDF membrane. Anti-H3K9ac (Millipore, 07-352) and anti-H3K9cr (PTM Biolabs, PTM-516) were diluted to 1:2000 and 1:1000, respectively, in 1x Superblock (ThermoScientific). An HRP-conjugated anti-rabbit (GE Healthcare) was used for detection. Bands were quantified using the ImageJ program. Dot blotting Increasing concentrations of biotinylated histone peptides (0.06–1.5 μg) were spotted onto a PVDF membrane then probed with the anti-H3K9ac (Millipore, 07-352) or H3K9cr (PTM Biolabs, PTM-516) at 1:2000 in a 5% non-fat milk solution and detected with an HRP-conjugated anti-rabbit by enhanced chemiluminesence (ECL). Bromodomains pull-downs cDNAs of GST-fused bromodomains were obtained either from EpiCypher Inc. or as a kind gift from Katrin Chua (Stanford University). GST fusions were expressed as described above except that the preparation buffer contained 50 mM Tris (pH 7.5), 150 mM NaCl, 10% glycerol (v/v), and 1 mM DTT. Pull-down assays were preformed as described above except that the assay buffer contained 50 mM Tris (pH 8.0), 300 mM NaCl, and 0.1% NP-40. Supplementary Material Accession codes. Coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 5IOK. Author contributions F.H.A., S.A.S., E.K.S., J.B.B., A.G., I.K.T and K.K. performed experiments and together with X.S., B.D.S and T.G.K. analyzed the data. F.H.A., S.A.S., B.D.S. and T.G.K. wrote the manuscript with input from all authors. Competing Financial Interest The authors declare no competing financial interests. Additional information Any supplementary information is available in the online version of this paper. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation Protein lysine acylation and cysteine succination by intermediates of energy metabolism Identification of ‘erasers’ for lysine crotonylated histone marks using a chemical proteomics approach Perceiving the epigenetic landscape through histone readers Interpreting the language of histone and DNA modifications A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications Histone recognition and large-scale structural analysis of the human bromodomain family YEATS domain proteins: a diverse family with many links to chromatin modification and transcription AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response Anc1 interacts with the catalytic subunits of the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes RSC and INO80, and the histone acetyltransferase complex NuA3 Preparation and analysis of the INO80 complex TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9 The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex The essential role of acetyllysine binding by the YEATS domain in transcriptional regulation Phaser crystallographic software PHENIX: a comprehensive Python-based system for macromolecular structure solution Features and development of Coot Molecular basis for chromatin binding and regulation of MLL5 Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4 A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery The structural mechanism for the recognition of H3K9cr (a) Chemical structure of crotonyllysine. (b) The crystal structure of the Taf14 YEATS domain (wheat) in complex with the H3K9cr5-13 peptide (green). (c) H3K9cr is stabilized via an extensive network of intermolecular electrostatic and polar interactions with the Taf14 YEATS domain. (d) The π-π-π stacking mechanism involving the alkene moiety of crotonyllysine. H3K9cr is a selective target of the Taf14 YEATS domain (a, b) Western blot analysis comparing the levels of H3K9cr and H3K9ac in wild type (WT), HAT deletion, or HDAC deletion yeast strains. Total H3 was used as a loading control. (c) Superimposed 1H,15N HSQC spectra of Taf14 YEATS recorded as H3K9cr5-13 and H3K9ac5-13 peptides were titrated in. Spectra are color coded according to the protein:peptide molar ratio. (d) Western blot analyses of peptide pull-down assays using wild-type and mutated Taf14 YEATS domains and indicated peptides.","denotations":[{"span":{"begin":4,"end":9},"obj":"0.99879897,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"1"},{"span":{"begin":10,"end":22},"obj":"0.9920379,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"2"},{"span":{"begin":38,"end":45},"obj":"0.9768092,protein_type,cleaner0,2023-07-04T16:21:00Z,MESH:","id":"3"},{"span":{"begin":46,"end":59},"obj":"0.60347056,ptm,cleaner0,2023-07-04T16:18:43Z,MESH:","id":"4"},{"span":{"begin":81,"end":88},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"553"},{"span":{"begin":259,"end":271},"obj":"0.98157585,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"5"},{"span":{"begin":298,"end":305},"obj":"0.6092492,protein_type,cleaner0,2023-07-04T16:21:00Z,MESH:","id":"6"},{"span":{"begin":306,"end":312},"obj":"0.64678025,residue_name,cleaner0,2023-07-05T08:52:59Z,SO:","id":"7"},{"span":{"begin":313,"end":326},"obj":"0.7005873,ptm,cleaner0,2023-07-04T16:18:43Z,MESH:","id":"8"},{"span":{"begin":408,"end":413},"obj":"0.9987513,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"9"},{"span":{"begin":414,"end":426},"obj":"0.98611736,structure_element,cleaner0,2023-07-04T16:20:27Z,SO:","id":"10"},{"span":{"begin":435,"end":449},"obj":"0.99818015,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"11"},{"span":{"begin":503,"end":516},"obj":"0.8457508,structure_element,cleaner0,2023-07-05T08:49:39Z,SO:","id":"12"},{"span":{"begin":522,"end":536},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"542"},{"span":{"begin":560,"end":573},"obj":"0.97012514,ptm,cleaner0,2023-07-04T16:18:43Z,MESH:","id":"13"},{"span":{"begin":577,"end":583},"obj":"0.8647513,residue_name,cleaner0,2023-07-05T08:53:04Z,SO:","id":"14"},{"span":{"begin":594,"end":608},"obj":"0.99726224,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"15"},{"span":{"begin":610,"end":613},"obj":"0.9968893,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"16"},{"span":{"begin":653,"end":660},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"554"},{"span":{"begin":710,"end":719},"obj":"0.9958947,taxonomy_domain,cleaner0,2023-07-04T16:21:35Z,DUMMY:","id":"17"},{"span":{"begin":834,"end":848},"obj":"0.7653515,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"18"},{"span":{"begin":857,"end":864},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"555"},{"span":{"begin":865,"end":867},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:36:55Z","id":"666"},{"span":{"begin":867,"end":870},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:37:14Z","id":"667"},{"span":{"begin":886,"end":890},"obj":"0.98865753,protein,cleaner0,2023-07-04T16:20:32Z,PR:","id":"20"},{"span":{"begin":894,"end":919},"obj":"0.98868376,protein_type,cleaner0,2023-07-04T16:22:54Z,MESH:","id":"21"},{"span":{"begin":941,"end":952},"obj":"0.7823207,ptm,cleaner0,2023-07-04T16:18:49Z,MESH:","id":"22"},{"span":{"begin":1027,"end":1041},"obj":"0.9841765,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"23"},{"span":{"begin":1046,"end":1058},"obj":"0.9894874,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"24"},{"span":{"begin":1060,"end":1063},"obj":"0.98921156,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"25"},{"span":{"begin":1129,"end":1133},"obj":"0.9711801,protein,cleaner0,2023-07-04T16:20:33Z,PR:","id":"26"},{"span":{"begin":1144,"end":1151},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"557"},{"span":{"begin":1152,"end":1165},"obj":"0.9621592,ptm,cleaner0,2023-07-04T16:18:43Z,MESH:","id":"27"},{"span":{"begin":1258,"end":1262},"obj":"0.9124805,protein,cleaner0,2023-07-04T16:20:33Z,PR:","id":"28"},{"span":{"begin":1273,"end":1284},"obj":"0.87436926,ptm,cleaner0,2023-07-04T16:18:49Z,MESH:","id":"29"},{"span":{"begin":1339,"end":1353},"obj":"0.91712606,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"30"},{"span":{"begin":1358,"end":1370},"obj":"0.9561159,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"31"},{"span":{"begin":1453,"end":1465},"obj":"0.8240044,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"32"},{"span":{"begin":1539,"end":1553},"obj":"0.6335516,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"33"},{"span":{"begin":1609,"end":1621},"obj":"0.94788533,structure_element,cleaner0,2023-07-04T16:21:48Z,SO:","id":"34"},{"span":{"begin":1623,"end":1626},"obj":"0.8961469,structure_element,cleaner0,2023-07-04T16:21:53Z,SO:","id":"35"},{"span":{"begin":1655,"end":1657},"obj":"0.92061985,structure_element,cleaner0,2023-07-05T08:51:22Z,SO:","id":"36"},{"span":{"begin":1688,"end":1700},"obj":"0.9774638,protein_state,cleaner0,2023-07-04T16:22:06Z,DUMMY:","id":"37"},{"span":{"begin":1743,"end":1753},"obj":"0.98200285,protein_state,cleaner0,2023-07-04T16:22:11Z,DUMMY:","id":"39"},{"span":{"begin":1779,"end":1791},"obj":"0.7515075,structure_element,cleaner0,2023-07-04T16:21:48Z,SO:","id":"41"},{"span":{"begin":1832,"end":1846},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"543"},{"span":{"begin":1879,"end":1891},"obj":"0.9015483,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"42"},{"span":{"begin":1946,"end":1951},"obj":"0.9973253,structure_element,cleaner0,2023-07-05T08:51:28Z,SO:","id":"43"},{"span":{"begin":1953,"end":1957},"obj":"0.99829453,protein,cleaner0,2023-07-05T07:54:03Z,PR:","id":"44"},{"span":{"begin":1959,"end":1962},"obj":"0.99791545,protein,cleaner0,2023-07-05T07:54:08Z,PR:","id":"45"},{"span":{"begin":1964,"end":1967},"obj":"0.9983627,protein,cleaner0,2023-07-05T07:54:14Z,PR:","id":"46"},{"span":{"begin":1969,"end":1974},"obj":"0.9985991,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"47"},{"span":{"begin":1976,"end":1980},"obj":"0.9987198,protein,cleaner0,2023-07-05T07:54:25Z,PR:","id":"48"},{"span":{"begin":1993,"end":1998},"obj":"0.96409446,species,cleaner0,2023-07-04T16:22:25Z,MESH:","id":"49"},{"span":{"begin":1999,"end":2002},"obj":"0.99878556,protein,cleaner0,2023-07-05T07:54:15Z,PR:","id":"50"},{"span":{"begin":2007,"end":2012},"obj":"0.9893267,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"51"},{"span":{"begin":2013,"end":2018},"obj":"0.9988275,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"52"},{"span":{"begin":2050,"end":2057},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"558"},{"span":{"begin":2063,"end":2065},"obj":"protein_type,MESH:,cleaner0,2023-07-05T07:55:54Z","id":"585"},{"span":{"begin":2065,"end":2069},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T07:56:23Z","id":"589"},{"span":{"begin":2075,"end":2087},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"547"},{"span":{"begin":2112,"end":2115},"obj":"0.99856865,protein,cleaner0,2023-07-05T07:54:15Z,PR:","id":"54"},{"span":{"begin":2116,"end":2128},"obj":"0.9379061,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"55"},{"span":{"begin":2169,"end":2194},"obj":"0.9904277,protein_type,cleaner0,2023-07-04T16:22:40Z,MESH:","id":"56"},{"span":{"begin":2195,"end":2200},"obj":"0.99846435,protein,cleaner0,2023-07-05T07:57:04Z,PR:","id":"57"},{"span":{"begin":2204,"end":2206},"obj":"protein_type,MESH:,cleaner0,2023-07-05T07:56:42Z","id":"590"},{"span":{"begin":2206,"end":2210},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T07:56:57Z","id":"591"},{"span":{"begin":2240,"end":2245},"obj":"0.9973254,protein,cleaner0,2023-07-05T07:57:04Z,PR:","id":"59"},{"span":{"begin":2255,"end":2257},"obj":"protein_type,MESH:,cleaner0,2023-07-05T07:57:26Z","id":"592"},{"span":{"begin":2257,"end":2260},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T07:57:40Z","id":"593"},{"span":{"begin":2261,"end":2272},"obj":"ptm,MESH:,cleaner0,2023-07-05T07:57:58Z","id":"594"},{"span":{"begin":2360,"end":2365},"obj":"0.9963744,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"61"},{"span":{"begin":2378,"end":2390},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"548"},{"span":{"begin":2415,"end":2420},"obj":"0.9987602,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"62"},{"span":{"begin":2421,"end":2433},"obj":"0.94719505,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"63"},{"span":{"begin":2480,"end":2485},"obj":"0.9980909,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"64"},{"span":{"begin":2559,"end":2564},"obj":"0.84213173,complex_assembly,cleaner0,2023-07-04T16:23:51Z,GO:","id":"67"},{"span":{"begin":2569,"end":2574},"obj":"0.6936775,complex_assembly,cleaner0,2023-07-04T16:24:02Z,GO:","id":"68"},{"span":{"begin":2585,"end":2590},"obj":"0.9974746,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"69"},{"span":{"begin":2658,"end":2663},"obj":"0.7698535,complex_assembly,cleaner0,2023-07-05T07:58:48Z,GO:","id":"71"},{"span":{"begin":2665,"end":2672},"obj":"0.67576855,complex_assembly,cleaner0,2023-07-05T07:58:53Z,GO:","id":"72"},{"span":{"begin":2677,"end":2680},"obj":"0.5300177,complex_assembly,cleaner0,2023-07-05T07:59:00Z,GO:","id":"73"},{"span":{"begin":2690,"end":2715},"obj":"0.8560897,protein_type,cleaner0,2023-07-04T16:22:53Z,MESH:","id":"74"},{"span":{"begin":2724,"end":2728},"obj":"0.77899855,complex_assembly,cleaner0,2023-07-05T08:50:53Z,GO:","id":"76"},{"span":{"begin":2764,"end":2769},"obj":"0.99761933,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"77"},{"span":{"begin":2856,"end":2861},"obj":"0.9986816,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"78"},{"span":{"begin":2862,"end":2874},"obj":"0.93180734,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"79"},{"span":{"begin":2890,"end":2904},"obj":"0.9986914,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"80"},{"span":{"begin":2919,"end":2926},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"561"},{"span":{"begin":2927,"end":2929},"obj":"protein_type,MESH:,cleaner0,2023-07-05T07:55:54Z","id":"586"},{"span":{"begin":2930,"end":2942},"obj":"0.6754686,protein_state,cleaner0,2023-07-04T16:22:07Z,DUMMY:","id":"82"},{"span":{"begin":2946,"end":2954},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T07:58:27Z","id":"595"},{"span":{"begin":2956,"end":2958},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:00:12Z","id":"597"},{"span":{"begin":2958,"end":2962},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T07:59:41Z","id":"598"},{"span":{"begin":3015,"end":3017},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:00:12Z","id":"599"},{"span":{"begin":3017,"end":3021},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:00:29Z","id":"600"},{"span":{"begin":3036,"end":3041},"obj":"0.9966305,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"87"},{"span":{"begin":3128,"end":3130},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:00:50Z","id":"601"},{"span":{"begin":3130,"end":3134},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:01:02Z","id":"602"},{"span":{"begin":3155,"end":3172},"obj":"0.9973307,evidence,cleaner0,2023-07-05T08:56:20Z,DUMMY:","id":"89"},{"span":{"begin":3180,"end":3185},"obj":"0.9986278,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"90"},{"span":{"begin":3186,"end":3198},"obj":"0.9957862,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"91"},{"span":{"begin":3199,"end":3214},"obj":"0.9311703,protein_state,cleaner0,2023-07-05T08:53:17Z,DUMMY:","id":"92"},{"span":{"begin":3215,"end":3225},"obj":"0.97627616,chemical,cleaner0,2023-07-05T08:36:15Z,CHEBI:","id":"93"},{"span":{"begin":3236,"end":3240},"obj":"0.96639997,residue_range,cleaner0,2023-07-05T08:49:48Z,DUMMY:","id":"94"},{"span":{"begin":3244,"end":3246},"obj":"0.9895627,protein_type,cleaner0,2023-07-05T07:55:54Z,MESH:","id":"95"},{"span":{"begin":3341,"end":3346},"obj":"0.998461,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"97"},{"span":{"begin":3347,"end":3359},"obj":"0.9965588,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"98"},{"span":{"begin":3370,"end":3403},"obj":"0.99343634,structure_element,cleaner0,2023-07-05T08:51:32Z,SO:","id":"99"},{"span":{"begin":3421,"end":3444},"obj":"0.96191806,structure_element,cleaner0,2023-07-05T08:51:36Z,SO:","id":"100"},{"span":{"begin":3461,"end":3466},"obj":"0.6941337,structure_element,cleaner0,2023-07-05T08:51:44Z,SO:","id":"102"},{"span":{"begin":3479,"end":3491},"obj":"0.9979013,site,cleaner0,2023-07-05T08:51:58Z,SO:","id":"103"},{"span":{"begin":3496,"end":3498},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:01:22Z","id":"603"},{"span":{"begin":3498,"end":3502},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:01:34Z","id":"604"},{"span":{"begin":3518,"end":3520},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:01:47Z","id":"605"},{"span":{"begin":3520,"end":3524},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:01:58Z","id":"606"},{"span":{"begin":3544,"end":3565},"obj":"0.9527997,protein_state,cleaner0,2023-07-05T08:53:22Z,DUMMY:","id":"106"},{"span":{"begin":3602,"end":3611},"obj":"0.99544466,structure_element,cleaner0,2023-07-05T08:51:48Z,SO:","id":"107"},{"span":{"begin":3774,"end":3788},"obj":"0.9968951,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"108"},{"span":{"begin":3841,"end":3853},"obj":"0.884992,protein_state,cleaner0,2023-07-04T16:22:07Z,DUMMY:","id":"109"},{"span":{"begin":3854,"end":3860},"obj":"0.98747534,residue_name,cleaner0,2023-07-05T08:02:11Z,SO:","id":"110"},{"span":{"begin":3903,"end":3907},"obj":"0.99885833,residue_name_number,cleaner0,2023-07-05T08:02:22Z,DUMMY:","id":"112"},{"span":{"begin":3952,"end":3962},"obj":"0.9932809,structure_element,cleaner0,2023-07-05T08:52:02Z,SO:","id":"114"},{"span":{"begin":4090,"end":4095},"obj":"0.99896455,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"115"},{"span":{"begin":4100,"end":4105},"obj":"0.99897707,residue_name_number,cleaner0,2023-07-05T08:02:31Z,DUMMY:","id":"116"},{"span":{"begin":4465,"end":4470},"obj":"0.99895763,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"117"},{"span":{"begin":4709,"end":4714},"obj":"0.9987826,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"118"},{"span":{"begin":5333,"end":5338},"obj":"0.9991684,residue_name_number,cleaner0,2023-07-05T08:02:41Z,DUMMY:","id":"119"},{"span":{"begin":5368,"end":5373},"obj":"0.9991742,residue_name_number,cleaner0,2023-07-05T08:02:45Z,DUMMY:","id":"120"},{"span":{"begin":5411,"end":5416},"obj":"0.9991697,residue_name_number,cleaner0,2023-07-05T08:02:44Z,DUMMY:","id":"121"},{"span":{"begin":5485,"end":5489},"obj":"0.9990522,residue_name_number,cleaner0,2023-07-05T08:02:22Z,DUMMY:","id":"122"},{"span":{"begin":5538,"end":5543},"obj":"0.99915934,residue_name_number,cleaner0,2023-07-05T08:02:45Z,DUMMY:","id":"123"},{"span":{"begin":5621,"end":5625},"obj":"0.9990495,residue_name_number,cleaner0,2023-07-05T08:02:22Z,DUMMY:","id":"124"},{"span":{"begin":5686,"end":5691},"obj":"0.99916136,residue_name_number,cleaner0,2023-07-05T08:02:52Z,DUMMY:","id":"125"},{"span":{"begin":5716,"end":5720},"obj":"0.9988856,residue_name_number,cleaner0,2023-07-05T08:02:22Z,DUMMY:","id":"126"},{"span":{"begin":5816,"end":5821},"obj":"0.9991516,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"127"},{"span":{"begin":5836,"end":5841},"obj":"0.9917144,chemical,cleaner0,2023-07-05T08:55:01Z,CHEBI:","id":"128"},{"span":{"begin":5901,"end":5906},"obj":"0.99916196,residue_name_number,cleaner0,2023-07-05T08:02:57Z,DUMMY:","id":"129"},{"span":{"begin":5981,"end":5986},"obj":"0.9983511,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"130"},{"span":{"begin":5987,"end":6017},"obj":"0.9934926,site,cleaner0,2023-07-05T08:03:03Z,SO:","id":"131"},{"span":{"begin":6036,"end":6076},"obj":"0.9922565,experimental_method,cleaner0,2023-07-05T08:03:06Z,MESH:","id":"132"},{"span":{"begin":6149,"end":6154},"obj":"0.99884135,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"133"},{"span":{"begin":6155,"end":6167},"obj":"0.94870484,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"134"},{"span":{"begin":6171,"end":6173},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:03:24Z","id":"607"},{"span":{"begin":6173,"end":6177},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:03:37Z","id":"608"},{"span":{"begin":6193,"end":6214},"obj":"0.995806,evidence,cleaner0,2023-07-05T08:03:41Z,DUMMY:","id":"136"},{"span":{"begin":6216,"end":6218},"obj":"0.9937781,evidence,cleaner0,2023-07-05T08:03:45Z,DUMMY:","id":"137"},{"span":{"begin":6228,"end":6250},"obj":"0.9887676,complex_assembly,cleaner0,2023-07-05T08:35:55Z,GO:","id":"138"},{"span":{"begin":6298,"end":6323},"obj":"0.9937454,experimental_method,cleaner0,2023-07-05T08:04:07Z,MESH:","id":"139"},{"span":{"begin":6379,"end":6397},"obj":"0.99432206,evidence,cleaner0,2023-07-05T08:04:01Z,DUMMY:","id":"140"},{"span":{"begin":6497,"end":6499},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:04:40Z","id":"609"},{"span":{"begin":6499,"end":6503},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:04:52Z","id":"610"},{"span":{"begin":6519,"end":6524},"obj":"0.9988524,protein,cleaner0,2023-07-04T16:20:21Z,PR:","id":"143"},{"span":{"begin":6548,"end":6550},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:08:27Z","id":"611"},{"span":{"begin":6550,"end":6554},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:08:52Z","id":"612"},{"span":{"begin":6569,"end":6574},"obj":"0.99658173,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"145"},{"span":{"begin":6589,"end":6608},"obj":"0.8414014,experimental_method,cleaner0,2023-07-05T08:57:36Z,MESH:","id":"146"},{"span":{"begin":6638,"end":6643},"obj":"0.9963198,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"147"},{"span":{"begin":6672,"end":6693},"obj":"0.9293416,experimental_method,cleaner0,2023-07-05T08:57:39Z,MESH:","id":"148"},{"span":{"begin":6728,"end":6730},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:09:10Z","id":"613"},{"span":{"begin":6730,"end":6734},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:09:22Z","id":"614"},{"span":{"begin":6736,"end":6738},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:09:38Z","id":"615"},{"span":{"begin":6738,"end":6742},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:09:50Z","id":"616"},{"span":{"begin":6747,"end":6749},"obj":"0.7814144,protein_type,cleaner0,2023-07-05T07:55:54Z,MESH:","id":"151"},{"span":{"begin":6817,"end":6819},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:10:08Z","id":"617"},{"span":{"begin":6819,"end":6823},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:10:21Z","id":"618"},{"span":{"begin":6828,"end":6830},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:10:36Z","id":"619"},{"span":{"begin":6830,"end":6834},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:10:54Z","id":"620"},{"span":{"begin":6852,"end":6857},"obj":"0.99671257,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"154"},{"span":{"begin":6858,"end":6866},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:57:52Z","id":"690"},{"span":{"begin":6914,"end":6916},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:38:01Z","id":"668"},{"span":{"begin":6916,"end":6920},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:38:14Z","id":"669"},{"span":{"begin":6934,"end":6939},"obj":"0.9966935,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"156"},{"span":{"begin":6958,"end":6960},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:38:30Z","id":"670"},{"span":{"begin":6960,"end":6964},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:38:42Z","id":"671"},{"span":{"begin":6996,"end":7022},"obj":"0.99616396,protein_type,cleaner0,2023-07-05T08:06:46Z,MESH:","id":"158"},{"span":{"begin":7024,"end":7028},"obj":"0.9961572,protein_type,cleaner0,2023-07-05T08:06:50Z,MESH:","id":"159"},{"span":{"begin":7034,"end":7054},"obj":"0.99562824,protein_type,cleaner0,2023-07-05T08:07:02Z,MESH:","id":"160"},{"span":{"begin":7056,"end":7061},"obj":"0.9862266,protein_type,cleaner0,2023-07-05T08:07:06Z,MESH:","id":"161"},{"span":{"begin":7114,"end":7119},"obj":"0.9961592,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"163"},{"span":{"begin":7141,"end":7146},"obj":"0.99671113,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"164"},{"span":{"begin":7147,"end":7151},"obj":"0.9969458,protein_type,cleaner0,2023-07-05T08:06:51Z,MESH:","id":"165"},{"span":{"begin":7153,"end":7157},"obj":"0.99758315,protein,cleaner0,2023-07-05T08:07:12Z,PR:","id":"166"},{"span":{"begin":7159,"end":7163},"obj":"0.9978067,protein,cleaner0,2023-07-05T08:07:16Z,PR:","id":"167"},{"span":{"begin":7169,"end":7175},"obj":"0.9977192,protein,cleaner0,2023-07-05T08:07:20Z,PR:","id":"168"},{"span":{"begin":7180,"end":7185},"obj":"0.9930031,protein_type,cleaner0,2023-07-05T08:07:06Z,MESH:","id":"169"},{"span":{"begin":7187,"end":7191},"obj":"0.99792385,protein,cleaner0,2023-07-05T08:07:24Z,PR:","id":"170"},{"span":{"begin":7193,"end":7197},"obj":"0.99804014,protein,cleaner0,2023-07-05T08:07:27Z,PR:","id":"171"},{"span":{"begin":7203,"end":7207},"obj":"0.9978777,protein,cleaner0,2023-07-05T08:07:31Z,PR:","id":"172"},{"span":{"begin":7214,"end":7221},"obj":"0.53316224,experimental_method,cleaner0,2023-07-05T09:00:08Z,MESH:","id":"173"},{"span":{"begin":7275,"end":7277},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:11:11Z","id":"621"},{"span":{"begin":7277,"end":7281},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:11:24Z","id":"622"},{"span":{"begin":7335,"end":7338},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:58:28Z","id":"691"},{"span":{"begin":7339,"end":7347},"obj":"0.47926757,experimental_method,cleaner0,2023-07-05T09:00:12Z,MESH:","id":"175"},{"span":{"begin":7405,"end":7409},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:58:22Z","id":"692"},{"span":{"begin":7410,"end":7418},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T09:04:29Z","id":"695"},{"span":{"begin":7461,"end":7463},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:11:41Z","id":"623"},{"span":{"begin":7463,"end":7467},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:12:06Z","id":"624"},{"span":{"begin":7536,"end":7538},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:12:21Z","id":"625"},{"span":{"begin":7538,"end":7542},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:12:32Z","id":"626"},{"span":{"begin":7587,"end":7589},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:12:47Z","id":"627"},{"span":{"begin":7589,"end":7593},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:13:00Z","id":"628"},{"span":{"begin":7628,"end":7633},"obj":"0.9963509,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"179"},{"span":{"begin":7725,"end":7729},"obj":"0.9969043,protein_type,cleaner0,2023-07-05T08:06:51Z,MESH:","id":"180"},{"span":{"begin":7734,"end":7739},"obj":"0.9925954,protein_type,cleaner0,2023-07-05T08:07:06Z,MESH:","id":"181"},{"span":{"begin":7777,"end":7787},"obj":"protein_state,DUMMY:,cleaner0,2023-07-04T16:22:11Z","id":"584"},{"span":{"begin":7788,"end":7795},"obj":"protein_type,MESH:,cleaner0,2023-07-04T16:21:00Z","id":"565"},{"span":{"begin":7807,"end":7812},"obj":"0.9988348,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"182"},{"span":{"begin":7813,"end":7825},"obj":"0.9854789,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"183"},{"span":{"begin":7834,"end":7844},"obj":"0.9957682,protein_state,cleaner0,2023-07-04T16:22:11Z,DUMMY:","id":"184"},{"span":{"begin":7845,"end":7847},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:13:59Z","id":"630"},{"span":{"begin":7847,"end":7849},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:14:10Z","id":"631"},{"span":{"begin":7904,"end":7906},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:14:26Z","id":"632"},{"span":{"begin":7906,"end":7910},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:14:39Z","id":"633"},{"span":{"begin":7939,"end":7944},"obj":"0.99873716,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"187"},{"span":{"begin":7953,"end":7967},"obj":"0.9983891,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"188"},{"span":{"begin":7989,"end":8000},"obj":"0.9863785,experimental_method,cleaner0,2023-07-05T08:18:57Z,MESH:","id":"189"},{"span":{"begin":8030,"end":8040},"obj":"0.990856,chemical,cleaner0,2023-07-05T08:36:15Z,CHEBI:","id":"190"},{"span":{"begin":8044,"end":8054},"obj":"0.9934884,chemical,cleaner0,2023-07-05T08:38:55Z,CHEBI:","id":"191"},{"span":{"begin":8067,"end":8075},"obj":"0.96406466,experimental_method,cleaner0,2023-07-05T09:00:19Z,MESH:","id":"193"},{"span":{"begin":8085,"end":8096},"obj":"protein_state,DUMMY:,cleaner0,2023-07-05T08:53:55Z","id":"688"},{"span":{"begin":8097,"end":8102},"obj":"0.9987318,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"195"},{"span":{"begin":8103,"end":8115},"obj":"0.98387945,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"196"},{"span":{"begin":8167,"end":8169},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:15:14Z","id":"636"},{"span":{"begin":8169,"end":8173},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:15:26Z","id":"637"},{"span":{"begin":8182,"end":8199},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T08:59:29Z","id":"694"},{"span":{"begin":8231,"end":8234},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T09:04:29Z","id":"693"},{"span":{"begin":8305,"end":8307},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:15:40Z","id":"638"},{"span":{"begin":8307,"end":8311},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:15:54Z","id":"639"},{"span":{"begin":8412,"end":8422},"obj":"0.49922895,evidence,cleaner0,2023-07-05T08:56:27Z,DUMMY:","id":"199"},{"span":{"begin":8426,"end":8431},"obj":"0.99908006,residue_name_number,cleaner0,2023-07-05T08:15:58Z,DUMMY:","id":"200"},{"span":{"begin":8436,"end":8441},"obj":"0.9990513,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"201"},{"span":{"begin":8449,"end":8461},"obj":"0.98532,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"202"},{"span":{"begin":8489,"end":8491},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:16:15Z","id":"640"},{"span":{"begin":8491,"end":8495},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:16:28Z","id":"641"},{"span":{"begin":8500,"end":8502},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:16:48Z","id":"642"},{"span":{"begin":8502,"end":8506},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:16:59Z","id":"643"},{"span":{"begin":8570,"end":8617},"obj":"site,SO:,cleaner0,2023-07-05T08:13:40Z","id":"629"},{"span":{"begin":8684,"end":8689},"obj":"0.998936,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"207"},{"span":{"begin":8747,"end":8749},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:17:15Z","id":"644"},{"span":{"begin":8749,"end":8753},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:17:29Z","id":"645"},{"span":{"begin":8774,"end":8776},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:17:45Z","id":"646"},{"span":{"begin":8776,"end":8780},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:17:57Z","id":"647"},{"span":{"begin":8953,"end":8965},"obj":"0.99369735,complex_assembly,cleaner0,2023-07-05T08:18:01Z,GO:","id":"210"},{"span":{"begin":9001,"end":9006},"obj":"0.99862266,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"211"},{"span":{"begin":9007,"end":9019},"obj":"0.9849653,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"212"},{"span":{"begin":9067,"end":9077},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"696"},{"span":{"begin":9098,"end":9123},"obj":"0.99509495,experimental_method,cleaner0,2023-07-05T09:00:34Z,MESH:","id":"213"},{"span":{"begin":9130,"end":9132},"obj":"0.99270695,protein_type,cleaner0,2023-07-05T07:55:54Z,MESH:","id":"214"},{"span":{"begin":9142,"end":9152},"obj":"0.9932382,protein_state,cleaner0,2023-07-04T16:22:11Z,DUMMY:","id":"216"},{"span":{"begin":9154,"end":9167},"obj":"0.956428,protein_state,cleaner0,2023-07-05T08:40:11Z,DUMMY:","id":"217"},{"span":{"begin":9169,"end":9180},"obj":"0.9795297,protein_state,cleaner0,2023-07-05T08:40:15Z,DUMMY:","id":"218"},{"span":{"begin":9186,"end":9198},"obj":"0.97335297,protein_state,cleaner0,2023-07-04T16:22:07Z,DUMMY:","id":"219"},{"span":{"begin":9202,"end":9210},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:18:20Z","id":"648"},{"span":{"begin":9221,"end":9225},"obj":"0.9283707,residue_range,cleaner0,2023-07-05T08:50:16Z,DUMMY:","id":"222"},{"span":{"begin":9229,"end":9231},"obj":"0.951781,protein_type,cleaner0,2023-07-05T07:55:54Z,MESH:","id":"223"},{"span":{"begin":9287,"end":9292},"obj":"0.99854577,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"224"},{"span":{"begin":9293,"end":9305},"obj":"0.98509496,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"225"},{"span":{"begin":9329,"end":9339},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T08:33:09Z","id":"649"},{"span":{"begin":9362,"end":9370},"obj":"0.78338593,protein_state,cleaner0,2023-07-05T08:54:04Z,DUMMY:","id":"228"},{"span":{"begin":9408,"end":9410},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:20:37Z","id":"653"},{"span":{"begin":9410,"end":9414},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:20:48Z","id":"654"},{"span":{"begin":9420,"end":9422},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:21:11Z","id":"655"},{"span":{"begin":9422,"end":9426},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:21:22Z","id":"656"},{"span":{"begin":9428,"end":9430},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:21:37Z","id":"657"},{"span":{"begin":9430,"end":9434},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:21:50Z","id":"658"},{"span":{"begin":9439,"end":9441},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:22:10Z","id":"659"},{"span":{"begin":9441,"end":9445},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:22:27Z","id":"660"},{"span":{"begin":9463,"end":9496},"obj":"0.98849183,experimental_method,cleaner0,2023-07-05T08:19:00Z,MESH:","id":"234"},{"span":{"begin":9510,"end":9520},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T08:33:21Z","id":"650"},{"span":{"begin":9522,"end":9532},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T08:33:34Z","id":"651"},{"span":{"begin":9538,"end":9548},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T08:33:45Z","id":"652"},{"span":{"begin":9565,"end":9593},"obj":"evidence,DUMMY:,cleaner0,2023-07-05T09:01:01Z","id":"697"},{"span":{"begin":9601,"end":9606},"obj":"0.9984143,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"241"},{"span":{"begin":9607,"end":9619},"obj":"0.9821952,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"242"},{"span":{"begin":9734,"end":9744},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T08:33:09Z","id":"663"},{"span":{"begin":9796,"end":9798},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:22:49Z","id":"661"},{"span":{"begin":9798,"end":9802},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:23:04Z","id":"662"},{"span":{"begin":9848,"end":9879},"obj":"0.99294585,experimental_method,cleaner0,2023-07-05T09:01:12Z,MESH:","id":"246"},{"span":{"begin":9904,"end":9909},"obj":"0.9990103,residue_name_number,cleaner0,2023-07-05T08:15:59Z,DUMMY:","id":"248"},{"span":{"begin":9986,"end":10000},"obj":"0.9981839,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"249"},{"span":{"begin":10145,"end":10152},"obj":"0.99031365,protein_state,cleaner0,2023-07-05T08:49:33Z,DUMMY:","id":"252"},{"span":{"begin":10153,"end":10158},"obj":"0.9989976,residue_name_number,cleaner0,2023-07-05T08:15:59Z,DUMMY:","id":"253"},{"span":{"begin":10195,"end":10205},"obj":"protein_state,DUMMY:,cleaner0,2023-07-05T09:01:51Z","id":"698"},{"span":{"begin":10206,"end":10211},"obj":"0.9989625,residue_name_number,cleaner0,2023-07-05T08:15:59Z,DUMMY:","id":"254"},{"span":{"begin":10257,"end":10265},"obj":"0.885494,protein_state,cleaner0,2023-07-05T08:54:04Z,DUMMY:","id":"255"},{"span":{"begin":10291,"end":10296},"obj":"0.9990196,residue_name_number,cleaner0,2023-07-05T08:15:59Z,DUMMY:","id":"257"},{"span":{"begin":10354,"end":10362},"obj":"0.9797934,experimental_method,cleaner0,2023-07-05T09:01:59Z,MESH:","id":"258"},{"span":{"begin":10366,"end":10371},"obj":"0.99903935,residue_name_number,cleaner0,2023-07-05T08:24:25Z,DUMMY:","id":"259"},{"span":{"begin":10410,"end":10415},"obj":"0.9990657,residue_name_number,cleaner0,2023-07-05T08:02:27Z,DUMMY:","id":"260"},{"span":{"begin":10515,"end":10529},"obj":"0.99843556,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"261"},{"span":{"begin":10533,"end":10542},"obj":"0.984743,protein_state,cleaner0,2023-07-05T08:54:12Z,DUMMY:","id":"262"},{"span":{"begin":10554,"end":10559},"obj":"0.99253696,species,cleaner0,2023-07-04T16:22:25Z,MESH:","id":"263"},{"span":{"begin":10560,"end":10573},"obj":"structure_element,SO:,cleaner0,2023-07-05T08:49:39Z","id":"684"},{"span":{"begin":10577,"end":10598},"obj":"0.9765474,experimental_method,cleaner0,2023-07-05T09:02:03Z,MESH:","id":"265"},{"span":{"begin":10625,"end":10635},"obj":"0.9461614,protein_state,cleaner0,2023-07-04T16:22:11Z,DUMMY:","id":"267"},{"span":{"begin":10637,"end":10650},"obj":"0.9879154,protein_state,cleaner0,2023-07-05T08:40:11Z,DUMMY:","id":"268"},{"span":{"begin":10652,"end":10663},"obj":"0.9869178,protein_state,cleaner0,2023-07-05T08:40:15Z,DUMMY:","id":"269"},{"span":{"begin":10669,"end":10681},"obj":"0.9762997,protein_state,cleaner0,2023-07-04T16:22:07Z,DUMMY:","id":"270"},{"span":{"begin":10682,"end":10689},"obj":"protein_type,MESH:,cleaner0,2023-07-05T09:02:17Z","id":"699"},{"span":{"begin":10741,"end":10754},"obj":"structure_element,SO:,cleaner0,2023-07-05T08:49:39Z","id":"685"},{"span":{"begin":10788,"end":10802},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"544"},{"span":{"begin":10883,"end":10889},"obj":"0.9987778,protein,cleaner0,2023-07-05T08:39:48Z,PR:","id":"275"},{"span":{"begin":10894,"end":10897},"obj":"0.99860966,protein,cleaner0,2023-07-05T07:54:09Z,PR:","id":"276"},{"span":{"begin":10925,"end":10937},"obj":"0.9837325,protein_state,cleaner0,2023-07-04T16:22:07Z,DUMMY:","id":"277"},{"span":{"begin":10948,"end":10953},"obj":"0.99857676,protein,cleaner0,2023-07-05T08:39:56Z,PR:","id":"279"},{"span":{"begin":10958,"end":10961},"obj":"0.9983223,protein,cleaner0,2023-07-05T07:54:15Z,PR:","id":"280"},{"span":{"begin":10968,"end":10976},"obj":"0.99105185,protein_state,cleaner0,2023-07-05T08:54:04Z,DUMMY:","id":"281"},{"span":{"begin":11018,"end":11030},"obj":"0.9855747,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"283"},{"span":{"begin":11040,"end":11059},"obj":"0.80789137,protein_type,cleaner0,2023-07-05T08:52:52Z,MESH:","id":"284"},{"span":{"begin":11061,"end":11072},"obj":"0.9922646,structure_element,cleaner0,2023-07-05T08:52:07Z,SO:","id":"285"},{"span":{"begin":11093,"end":11107},"obj":"0.99855334,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"286"},{"span":{"begin":11135,"end":11138},"obj":"0.7588632,structure_element,cleaner0,2023-07-04T16:21:53Z,SO:","id":"287"},{"span":{"begin":11142,"end":11163},"obj":"0.9541701,experimental_method,cleaner0,2023-07-05T09:02:34Z,MESH:","id":"288"},{"span":{"begin":11214,"end":11226},"obj":"0.99803704,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"289"},{"span":{"begin":11231,"end":11246},"obj":"0.9968952,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"290"},{"span":{"begin":11300,"end":11312},"obj":"0.9787652,structure_element,cleaner0,2023-07-04T16:21:48Z,SO:","id":"291"},{"span":{"begin":11400,"end":11414},"obj":"0.99844176,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"292"},{"span":{"begin":11434,"end":11437},"obj":"0.8739639,structure_element,cleaner0,2023-07-04T16:21:53Z,SO:","id":"293"},{"span":{"begin":11441,"end":11445},"obj":"0.99858606,protein,cleaner0,2023-07-05T08:51:13Z,PR:","id":"294"},{"span":{"begin":11450,"end":11454},"obj":"0.9986286,protein,cleaner0,2023-07-05T08:51:16Z,PR:","id":"295"},{"span":{"begin":11518,"end":11530},"obj":"0.98622835,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"296"},{"span":{"begin":11563,"end":11577},"obj":"0.9985879,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"297"},{"span":{"begin":11617,"end":11629},"obj":"0.99071395,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"298"},{"span":{"begin":11633,"end":11638},"obj":"0.9987459,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"299"},{"span":{"begin":11662,"end":11669},"obj":"0.5421235,protein_type,cleaner0,2023-07-04T16:21:00Z,MESH:","id":"300"},{"span":{"begin":11670,"end":11683},"obj":"0.672082,ptm,cleaner0,2023-07-04T16:18:43Z,MESH:","id":"301"},{"span":{"begin":11870,"end":11872},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:41:07Z","id":"672"},{"span":{"begin":11872,"end":11876},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:41:21Z","id":"673"},{"span":{"begin":11887,"end":11892},"obj":"0.99646616,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"303"},{"span":{"begin":11925,"end":11929},"obj":"0.9973616,protein_type,cleaner0,2023-07-05T08:06:51Z,MESH:","id":"304"},{"span":{"begin":11934,"end":11939},"obj":"0.9948607,protein_type,cleaner0,2023-07-05T08:07:06Z,MESH:","id":"305"},{"span":{"begin":11983,"end":11993},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"700"},{"span":{"begin":12009,"end":12014},"obj":"0.998776,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"306"},{"span":{"begin":12015,"end":12027},"obj":"0.9936651,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"307"},{"span":{"begin":12151,"end":12165},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"545"},{"span":{"begin":12217,"end":12222},"obj":"0.9987233,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"308"},{"span":{"begin":12250,"end":12264},"obj":"0.99826485,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"309"},{"span":{"begin":12269,"end":12281},"obj":"0.9959139,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"310"},{"span":{"begin":12341,"end":12355},"obj":"residue_name,SO:,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z","id":"546"},{"span":{"begin":12377,"end":12382},"obj":"0.9981281,protein_type,cleaner0,2023-07-05T08:52:37Z,MESH:","id":"311"},{"span":{"begin":20558,"end":20560},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:46:18Z","id":"674"},{"span":{"begin":20560,"end":20564},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:46:30Z","id":"675"},{"span":{"begin":20591,"end":20605},"obj":"0.99838877,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"502"},{"span":{"begin":20615,"end":20632},"obj":"0.99736893,evidence,cleaner0,2023-07-05T08:56:31Z,DUMMY:","id":"503"},{"span":{"begin":20640,"end":20645},"obj":"0.99835616,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"504"},{"span":{"begin":20646,"end":20658},"obj":"0.97807664,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"505"},{"span":{"begin":20667,"end":20682},"obj":"protein_state,DUMMY:,cleaner0,2023-07-05T08:54:40Z","id":"689"},{"span":{"begin":20687,"end":20697},"obj":"0.80304146,chemical,cleaner0,2023-07-05T08:36:15Z,CHEBI:","id":"507"},{"span":{"begin":20719,"end":20721},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:46:58Z","id":"676"},{"span":{"begin":20721,"end":20725},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:47:12Z","id":"677"},{"span":{"begin":20829,"end":20834},"obj":"0.99865216,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"510"},{"span":{"begin":20835,"end":20847},"obj":"0.9790957,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"511"},{"span":{"begin":20913,"end":20927},"obj":"0.9983652,residue_name,melaniev@ebi.ac.uk,2023-07-06T15:25:20Z,SO:","id":"512"},{"span":{"begin":20932,"end":20934},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:47:40Z","id":"678"},{"span":{"begin":20934,"end":20938},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:47:55Z","id":"679"},{"span":{"begin":20968,"end":20973},"obj":"0.9988475,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"514"},{"span":{"begin":20974,"end":20986},"obj":"0.9892417,structure_element,cleaner0,2023-07-04T16:20:28Z,SO:","id":"515"},{"span":{"begin":20994,"end":21006},"obj":"0.98307806,experimental_method,cleaner0,2023-07-05T09:03:32Z,MESH:","id":"516"},{"span":{"begin":21040,"end":21042},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:48:14Z","id":"680"},{"span":{"begin":21042,"end":21046},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:48:26Z","id":"681"},{"span":{"begin":21051,"end":21053},"obj":"protein_type,MESH:,cleaner0,2023-07-05T08:48:42Z","id":"682"},{"span":{"begin":21053,"end":21057},"obj":"residue_name_number,DUMMY:,cleaner0,2023-07-05T08:48:52Z","id":"683"},{"span":{"begin":21061,"end":21070},"obj":"0.9924296,protein_state,cleaner0,2023-07-05T08:49:13Z,DUMMY:","id":"519"},{"span":{"begin":21072,"end":21074},"obj":"0.98962665,protein_state,cleaner0,2023-07-05T08:49:18Z,DUMMY:","id":"520"},{"span":{"begin":21094,"end":21098},"obj":"protein_type,MESH:,cleaner0,2023-07-05T09:03:46Z","id":"701"},{"span":{"begin":21099,"end":21107},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T09:04:00Z","id":"702"},{"span":{"begin":21108,"end":21113},"obj":"0.99134904,taxonomy_domain,cleaner0,2023-07-04T16:22:20Z,DUMMY:","id":"521"},{"span":{"begin":21129,"end":21131},"obj":"0.9896226,protein_type,cleaner0,2023-07-05T07:55:54Z,MESH:","id":"522"},{"span":{"begin":21180,"end":21191},"obj":"0.90694416,experimental_method,cleaner0,2023-07-05T09:03:35Z,MESH:","id":"523"},{"span":{"begin":21192,"end":21199},"obj":"0.65750146,evidence,cleaner0,2023-07-05T08:57:05Z,DUMMY:","id":"524"},{"span":{"begin":21203,"end":21208},"obj":"0.9981918,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"525"},{"span":{"begin":21209,"end":21214},"obj":"0.99271107,structure_element,cleaner0,2023-07-05T08:52:13Z,SO:","id":"526"},{"span":{"begin":21227,"end":21237},"obj":"0.7894704,chemical,cleaner0,2023-07-05T08:36:15Z,CHEBI:","id":"527"},{"span":{"begin":21242,"end":21252},"obj":"chemical,CHEBI:,cleaner0,2023-07-05T08:38:55Z","id":"635"},{"span":{"begin":21267,"end":21275},"obj":"experimental_method,MESH:,cleaner0,2023-07-05T09:04:10Z","id":"703"},{"span":{"begin":21280,"end":21287},"obj":"0.6348235,evidence,cleaner0,2023-07-05T08:57:07Z,DUMMY:","id":"531"},{"span":{"begin":21354,"end":21366},"obj":"0.98869205,experimental_method,cleaner0,2023-07-05T08:49:22Z,MESH:","id":"532"},{"span":{"begin":21379,"end":21403},"obj":"0.99291915,experimental_method,cleaner0,2023-07-05T08:49:24Z,MESH:","id":"533"},{"span":{"begin":21410,"end":21419},"obj":"0.99699277,protein_state,cleaner0,2023-07-05T08:49:30Z,DUMMY:","id":"534"},{"span":{"begin":21424,"end":21431},"obj":"0.959159,protein_state,cleaner0,2023-07-05T08:49:33Z,DUMMY:","id":"535"},{"span":{"begin":21432,"end":21437},"obj":"0.9981369,protein,cleaner0,2023-07-04T16:20:22Z,PR:","id":"536"},{"span":{"begin":21438,"end":21451},"obj":"0.981699,structure_element,cleaner0,2023-07-05T08:49:39Z,SO:","id":"537"}],"relations":[]}]