RNA polymerase II-associated protein 3 (RPAP3) is a 665-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9H6T3.
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The mean pLDDT of this model is 74.3 (confident 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 | 41% |
| 70 to 90 | Confident: backbone generally right | 26% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 25% |
What pLDDT means and how to read it
Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation
Tightly associated with the RNA polymerase II complex (PubMed:17643375). Component of the R2TP complex composed at least of RUVBL1, RUVBL2, RPAP3 and PIHD1 (PubMed:20864032). Component of the PAQosome complex which is responsible for the biogenesis of several protein complexes and which consists of R2TP complex members RUVBL1, RUVBL2, RPAP3 and PIH1D1, URI complex members PFDN2, PFDN6, PDRG1,…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6ZBK | X-ray | 1.49 Å | A=133-255 |
| 6FM8 | X-ray | 1.78 Å | A=576-625 |
| 4CGV | X-ray | 2.54 Å | A/B/C/D=120-255 |
| 6GXZ | X-ray | 2.96 Å | A/C=281-445 |
| 4CGW | X-ray | 3.0 Å | A/B=265-381 |
| 6FO1 | EM | 3.57 Å | G=1-665 |
| 6EZ4 | NMR | A=535-665 | |
| 6FD7 | NMR | A=133-255 | |
| 6FDP | NMR | A=281-395 | |
| 6FDT | NMR | A=281-396 |
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