DNA-directed RNA polymerases I and III subunit RPAC1 (RPC40) is a 335-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P07703.
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The mean pLDDT of this model is 93.1 (very high overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 84% |
| 70 to 90 | Confident: backbone generally right | 14% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
DNA-dependent RNA polymerases catalyze the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I (Pol I) and III (Pol III) which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPC40 is part of the polymerase core and may function as a clamp element that moves to open and close the cleft (PubMed:18160037, PubMed:24153182, PubMed:24153184). Plays an important role in targeting retrotransposons Ty integration upstream of pol III-transcribed genes such as tRNA genes, allowing Ty1, Ty2 and Ty4 to proliferate and yet minimizing genetic damage (PubMed:25931562)
Component of the RNA polymerase I (Pol I) complex consisting of 14 subunits: RPA135, RPA190, RPC40, RPA14, RPB5, RPO26, RPA43, RPB8, RPA12, RPB10, RPC19, RPC10, RPA49 and RPA34 (PubMed:11717393, PubMed:12407181, PubMed:18160037, PubMed:24153182, PubMed:24153184, PubMed:8516295). The complex is composed of a horseshoe-shaped core containing ten subunits (RPA135, RPA190, RPB5, RPO26, RPB8, RPB10,…
Nucleus, nucleolus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7Z0H | EM | 2.6 Å | C=1-335 |
| 6RUI | EM | 2.7 Å | C=1-335 |
| 7Z1O | EM | 2.7 Å | C=1-335 |
| 9G1V | EM | 2.7 Å | C=1-335 |
| 7Z31 | EM | 2.76 Å | C=1-335 |
| 4C2M | X-ray | 2.8 Å | C/R=1-335 |
| 7Z1L | EM | 2.8 Å | C=1-335 |
| 9G27 | EM | 2.8 Å | C=1-335 |
| 6RQL | EM | 2.9 Å | C=1-335 |
| 7Z30 | EM | 2.9 Å | C=1-335 |
| 4C3I | X-ray | 3.0 Å | C=1-335 |
| 6RWE | EM | 3.0 Å | C=1-335 |
| 7Z2Z | EM | 3.07 Å | C=1-335 |
| 6RRD | EM | 3.1 Å | C=1-335 |
| 6HLQ | EM | 3.18 Å | C=1-335 |
| 6HLR | EM | 3.18 Å | C=1-335 |
| 8BWS | EM | 3.2 Å | C=1-335 |
| 9G2B | EM | 3.2 Å | C=1-335 |
| 6HLS | EM | 3.21 Å | C=1-335 |
| 6TUT | EM | 3.25 Å | C=1-335 |
Showing 20 of 70 experimental structures (best resolution first).
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