license: cc0-1.0
task_categories:
- text-generation
- fill-mask
- other
tags:
- RNA
- RNAcentral
- PDB
- mmCIF
- structural-biology
- inverse-folding
pretty_name: RNAcentral-Struct
size_categories:
- 1K<n<10K
RNAcentral-Struct
RNAcentral-Struct is a structure subset derived from the official RNAcentral PDB cross-reference table. It contains every unique PDB entry referenced by RNAcentral current_release/id_mapping/database_mappings/pdb.tsv, downloaded as mmCIF from official PDB mirrors.
This dataset is intended for RNA structure-conditioned modeling, inverse folding, and cross-reference analysis. RNAcentral itself is a sequence and annotation resource; the 3D coordinates here come from wwPDB/RCSB/PDBe entries linked by RNAcentral.
Contents
structures/*.cif: 7,279 unique mmCIF files, one per four-character PDB entry ID.metadata/rnacentral_pdb.tsv: the RNAcentral official PDB cross-reference table used to build this package.metadata/pdb_structure_mapping_all.csv: all RNAcentral chain-level mappings to the downloaded mmCIF files.metadata/pdb_structure_mapping_downloaded.csv: mappings whose referenced mmCIF file is present. For this release it matches the full mapping table.metadata/manifest.json: machine-readable summary.metadata/summary.tsv: compact summary.metadata/cif_sizes.tsv: byte size for each downloaded mmCIF file.metadata/download_failures.json: download failure list. This release has no failures.scripts/rnacentral_all_cif_downloader.py: downloader used to reproduce the package.
Summary
| field | value |
|---|---|
| RNAcentral PDB mapping rows | 18,967 |
| Unique RNAcentral UPI IDs | 4,750 |
| Unique PDB/mmCIF entries | 7,279 |
| Downloaded mmCIF files | 7,279 |
| Download failures | 0 |
| Uncompressed package size | ~54 GB |
Mapping Semantics
RNAcentral pdb.tsv maps RNAcentral UPI IDs to PDB chain-level accessions such as 4UG0_L8. The four-character prefix, 4UG0, is the PDB entry ID and corresponds to one mmCIF file: structures/4ug0.cif. The suffix identifies a chain or chain-like accession within that entry. Multiple RNAcentral rows can therefore reference the same mmCIF file.
Reproducibility
The source mapping file is:
https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/database_mappings/pdb.tsv
The downloader extracts unique PDB IDs from that mapping and downloads {PDB_ID}.cif from RCSB with PDBe fallback.
License
RNAcentral sequence metadata is distributed under CC0. PDB coordinate files are redistributed according to wwPDB/RCSB/PDBe terms. Please cite RNAcentral and wwPDB/PDB resources when using this dataset.
Citation
@article{rnacentral2021,
author = {{RNAcentral Consortium}},
title = {{RNAcentral} 2021: secondary structure integration, improved sequence search and new member databases},
journal = {Nucleic Acids Research},
volume = {49},
number = {D1},
pages = {D212--D220},
year = {2021},
doi = {10.1093/nar/gkaa921}
}