DNA-directed RNA polymerases I, II, and III subunit RPABC1 (RPB5) is a 215-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P20434.
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The mean pLDDT of this model is 94.1 (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 | 88% |
| 70 to 90 | Confident: backbone generally right | 12% |
| 50 to 70 | Low: treat with caution | 1% |
| 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, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. RNA polymerase complexes are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process
Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes. 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. The complex is composed of a horseshoe-shaped core containing ten subunits (RPA135, RPA190, RPB5, RPO26,…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1DZF | X-ray | 1.9 Å | A=1-215 |
| 1TWF | X-ray | 2.3 Å | E=1-215 |
| 9KD8 | EM | 2.46 Å | E=1-215 |
| 9K7F | EM | 2.5 Å | E=1-215 |
| 7Z0H | EM | 2.6 Å | E=1-215 |
| 9KDQ | EM | 2.63 Å | E=1-215 |
| 6RUI | EM | 2.7 Å | E=1-215 |
| 7Z1O | EM | 2.7 Å | E=1-215 |
| 8JCH | EM | 2.7 Å | E=1-215 |
| 9G1V | EM | 2.7 Å | E=1-215 |
| 7Z31 | EM | 2.76 Å | E=1-215 |
| 1I50 | X-ray | 2.8 Å | E=1-215 |
| 1K83 | X-ray | 2.8 Å | E=1-215 |
| 3CQZ | X-ray | 2.8 Å | E=1-215 |
| 4C2M | X-ray | 2.8 Å | E/T=1-215 |
| 7Z1L | EM | 2.8 Å | E=1-215 |
| 8K5P | EM | 2.8 Å | E=1-215 |
| 8RAM | EM | 2.8 Å | E=1-215 |
| 9G27 | EM | 2.8 Å | E=1-215 |
| 3S14 | X-ray | 2.85 Å | E=1-215 |
Showing 20 of 280 experimental structures (best resolution first).
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