Families Curated with 3D Structures
- Goal
- Enhance Rfam families that were annotated before a 3D structure was available, replacing predicted secondary structures with more accurate annotations derived from experimentally determined PDB structures.
- Status
- Ongoing — families are updated on a rolling basis as new structures become available. Download all 3D family seed alignments (Rfam.3d.seed.gz).
- Collaborators
- Protein Data Bank in Europe (PDBe)
Background
Many Rfam families were originally annotated years — in some cases six or more — before an experimental 3D structure was available for any of their members. As a result, these families carry predicted secondary structures that are less accurate than what the solved structures reveal.
About the Project
This project systematically revisits those families. Rfam connects families to experimentally determined 3D structures in two stages. Families with 3D structure reported are families that currently map to one or more PDB structures. A subset of those families (families with 3D information in SEED) have been manually re-curated so their SEED secondary-structure annotation reflects the base pairs, pseudoknots, and tertiary contacts seen in the structure. This page tracks both: every mapped family below, and the curated subset whose updated seeds ship in Rfam.3d.seed.gz.
Please contact us if you have questions or would like to suggest a family for 3D-guided curation.
All Families with a PDB Mapping
Every Rfam family with at least one experimentally determined structure in the Protein Data Bank, shown with the matching PDB entries. This list is generated automatically and updated with each Rfam release.
| Accession | Rfam ID | PDB ID | Chain | Bit score | E-value |
|---|---|---|---|---|---|
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Curated 3D Seed Alignments
Families whose SEED has been updated with annotation derived from the 3D structure. The PDB column lists the entries used in curation. Download individual seeds, or the full bundle Rfam.3d.seed.gz.
| Rfam ID ↕ | Description ↕ | PDB IDs | Download |
|---|
References
- Ontiveros-Palacios N, Cooke E, Nawrocki EP, Triebel S, Marz M, Rivas E, Griffiths-Jones S, Petrov AI, Bateman A, Sweeney B (2025) Rfam 15: RNA families database in 2025. Nucleic Acids Res 53(D1):D258–D267. doi: 10.1093/nar/gkae1023
- Rfam Help documentation. Integrating 3D Structures into a SEED Alignment. https://docs.rfam.org/en/latest/adding-3d-structures.html
