DNA-directed RNA polymerase II subunit RPB3 (RPB3) is a 318-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P16370.
Explore in 3D Color by confidence AlphaFold DB UniProt
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 | 81% |
| 70 to 90 | Confident: backbone generally right | 4% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 14% |
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. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination
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 | C=1-318 |
| 9KD8 | EM | 2.46 Å | C=1-318 |
| 9K7F | EM | 2.5 Å | C=1-318 |
| 9KDQ | EM | 2.63 Å | C=1-268 |
| 8JCH | EM | 2.7 Å | C=1-318 |
| 1I50 | X-ray | 2.8 Å | C=1-318 |
| 1K83 | X-ray | 2.8 Å | C=1-318 |
| 3CQZ | X-ray | 2.8 Å | C=1-318 |
| 8K5P | EM | 2.8 Å | C=1-318 |
| 8RAM | EM | 2.8 Å | C=1-318 |
| 3S14 | X-ray | 2.85 Å | C=1-318 |
| 9KD9 | EM | 2.88 Å | C=1-318 |
| 2NVQ | X-ray | 2.9 Å | C=1-318 |
| 7NKX | EM | 2.9 Å | C=1-318 |
| 7O4J | EM | 2.9 Å | C=4-318 |
| 7RIM | X-ray | 2.9 Å | C=1-318 |
| 9KDO | EM | 2.92 Å | C=1-318 |
| 6BM4 | X-ray | 2.95 Å | C=1-318 |
| 9KDN | EM | 2.96 Å | C=1-318 |
| 9JA1 | EM | 2.98 Å | C=1-318 |
Showing 20 of 209 experimental structures (best resolution first).
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.