DNA-directed RNA polymerase II subunit RPB2 (RPB2) is a 1224-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P08518.
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The mean pLDDT of this model is 87.3 (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 | 59% |
| 70 to 90 | Confident: backbone generally right | 32% |
| 50 to 70 | Low: treat with caution | 7% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are…
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1TWF | X-ray | 2.3 Å | B=1-1224 |
| 9KD8 | EM | 2.46 Å | B=1-1224 |
| 9K7F | EM | 2.5 Å | B=1-1224 |
| 9KDQ | EM | 2.63 Å | B=1-1224 |
| 8JCH | EM | 2.7 Å | B=1-1224 |
| 1I50 | X-ray | 2.8 Å | B=1-1224 |
| 1K83 | X-ray | 2.8 Å | B=1-1224 |
| 3CQZ | X-ray | 2.8 Å | B=1-1224 |
| 8K5P | EM | 2.8 Å | B=1-1224 |
| 8RAM | EM | 2.8 Å | B=1-1224 |
| 3S14 | X-ray | 2.85 Å | B=1-1224 |
| 9KD9 | EM | 2.88 Å | B=1-1224 |
| 2NVQ | X-ray | 2.9 Å | B=1-1224 |
| 7NKX | EM | 2.9 Å | B=1-1224 |
| 7O4J | EM | 2.9 Å | B=1-1224 |
| 7RIM | X-ray | 2.9 Å | B=1-1224 |
| 9KDO | EM | 2.92 Å | B=1-1224 |
| 6BM4 | X-ray | 2.95 Å | B=1-1224 |
| 9KDN | EM | 2.96 Å | B=1-1224 |
| 9JA1 | EM | 2.98 Å | B=1-1224 |
Showing 20 of 211 experimental structures (best resolution first).
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