---
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:

```text
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

```bibtex
@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}
}
```