DNA-directed RNA polymerase II subunit RPB1 (RPO21) is a 1733-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P04050.
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The mean pLDDT of this model is 81.4 (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 | 56% |
| 70 to 90 | Confident: backbone generally right | 24% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 15% |
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. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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 melted and the single-stranded DNA template strand of…
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits (PubMed:11805306, PubMed:12914699, PubMed:16341226). Interacts with DEF1; the interaction is direct and serves to bridge RPB1 to the Elongin complex in a DNA-damaged dependent manner (PubMed:23993092). Interacts with the Elongin subunit ELA1 (PubMed:23993092). Interacts with the Elongin subunit ELC1 (PubMed:23993092).…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5VKO | X-ray | 1.8 Å | B=1468-1500 |
| 5VKL | X-ray | 2.2 Å | B=1476-1498 |
| 1TWF | X-ray | 2.3 Å | A=1-1733 |
| 9KD8 | EM | 2.46 Å | A=1-1733 |
| 6NPW | X-ray | 2.49 Å | E=1672-1690 |
| 9K7F | EM | 2.5 Å | A=1-1733 |
| 9KDQ | EM | 2.63 Å | A=1-1454 |
| 8JCH | EM | 2.7 Å | A=1-1733 |
| 1I50 | X-ray | 2.8 Å | A=1-1733 |
| 1K83 | X-ray | 2.8 Å | A=1-1733 |
| 3CQZ | X-ray | 2.8 Å | A=1-1733 |
| 8K5P | EM | 2.8 Å | A=1-1733 |
| 8RAM | EM | 2.8 Å | A=1-1733 |
| 3S14 | X-ray | 2.85 Å | A=1-1733 |
| 9KD9 | EM | 2.88 Å | A=1-1733 |
| 2NVQ | X-ray | 2.9 Å | A=1-1733 |
| 7NKX | EM | 2.9 Å | A=1-1733 |
| 7O4J | EM | 2.9 Å | A=1-1733 |
| 7RIM | X-ray | 2.9 Å | A=1-1733 |
| 9KDO | EM | 2.92 Å | A=1-1733 |
Showing 20 of 222 experimental structures (best resolution first).
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