DNA-directed RNA polymerase II subunit RPB1 (POLR2A) is a 1970-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P24928.
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The mean pLDDT of this model is 76.0 (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 | 49% |
| 70 to 90 | Confident: backbone generally right | 23% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 25% |
What pLDDT means and how to read it
Catalytic core component of RNA polymerase II (Pol II), a DNA-dependent RNA polymerase which synthesizes mRNA precursors and many functional non-coding RNAs using the four ribonucleoside triphosphates as substrates (By similarity) (PubMed:23748380, PubMed:27193682, PubMed:30190596, PubMed:9852112). Pol II-mediated transcription cycle proceeds through transcription initiation, transcription elongation and transcription termination stages. During transcription initiation, Pol II pre-initiation complex (PIC) is recruited to DNA promoters, with focused-type promoters containing either the initiator (Inr) element, or the TATA-box found in cell-type specific genes and dispersed-type promoters…
Component of the RNA polymerase II (Pol II) core complex consisting of 12 subunits: a ten-subunit catalytic core composed of POLR2A/RPB1, POLR2B/RPB2, POLR2C/RPB3, POLR2I/RPB9, POLR2J/RPB11, POLR2E/RPABC1, POLR2F/RPABC2, POLR2H/RPABC3, POLR2K/RPABC4 and POLR2L/RPABC5 and a mobile stalk composed of two subunits POLR2D/RPB4 and POLR2G/RPB7, protruding from the core and functioning primarily in…
Nucleus, Cytoplasm, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6G0R | X-ray | 1.25 Å | C=772-782 |
| 7Z1K | X-ray | 1.55 Å | B=1788-1803 |
| 3D9N | X-ray | 1.6 Å | Y/Z=1790-1803 |
| 6XKB | X-ray | 1.6 Å | F/G/I/J/K=1786-1805 |
| 3D9M | X-ray | 1.75 Å | Y/Z=1790-1803 |
| 6IC9 | X-ray | 1.75 Å | C/D=1790-1803 |
| 2GHT | X-ray | 1.8 Å | C/D=1796-1803 |
| 4JXT | X-ray | 1.9 Å | B=1786-1805 |
| 6IC8 | X-ray | 1.93 Å | C/D=1790-1803 |
| 3D9O | X-ray | 2.0 Å | Z=1790-1803 |
| 2GHQ | X-ray | 2.05 Å | C/D=1795-1803 |
| 3D9P | X-ray | 2.1 Å | Y/Z=1790-1803 |
| 3D9K | X-ray | 2.2 Å | Y/Z=1790-1803 |
| 3D9L | X-ray | 2.2 Å | Y/Z=1790-1803 |
| 7Z42 | X-ray | 2.42 Å | G/I/X/Y=1713-1740 |
| 8PNP | EM | 2.49 Å | G=1699-1740 |
| 5M3H | X-ray | 2.5 Å | X/Y=1713-1740 |
| 9B9L | X-ray | 2.5 Å | C=1791-1805 |
| 9EHZ | EM | 2.6 Å | A=1-1970 |
| 8XSO | EM | 2.7 Å | A=1-1970 |
Showing 20 of 56 experimental structures (best resolution first).
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