StarLiu714/RNAcentral-Struct

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

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}
}