DNA-directed RNA polymerase II subunit RPB4 (RPB4) is a 221-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P20433.
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The mean pLDDT of this model is 85.3 (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 | 58% |
| 70 to 90 | Confident: backbone generally right | 24% |
| 50 to 70 | Low: treat with caution | 16% |
| Below 50 | Very low: often disordered regions | 1% |
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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RPB4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex…
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a dissociable subcomplex associated with the 10-subunit Pol II core complex. In exponentially proliferating cells, only approximately 20 % of the Pol II complexes contain the RPB4-RPB7 subcomplex. In starving cells, that enter stationary phase, RPB4-RPB7 is associated with Pol II in a stoichiometric…
Nucleus, Cytoplasm, Cytoplasm, P-body
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1Y14 | X-ray | 2.3 Å | A/C=35-221 |
| 9KD8 | EM | 2.46 Å | D=1-221 |
| 9K7F | EM | 2.5 Å | D=1-221 |
| 9KDQ | EM | 2.63 Å | D=1-221 |
| 8JCH | EM | 2.7 Å | D=1-221 |
| 8K5P | EM | 2.8 Å | D=1-221 |
| 8RAM | EM | 2.8 Å | D=1-221 |
| 9KD9 | EM | 2.88 Å | D=1-221 |
| 7NKX | EM | 2.9 Å | D=1-221 |
| 7O4J | EM | 2.9 Å | D=1-221 |
| 9KDO | EM | 2.92 Å | D=1-221 |
| 9KDN | EM | 2.96 Å | D=1-221 |
| 9JA1 | EM | 2.98 Å | D=1-221 |
| 7ML0 | EM | 3.0 Å | D=1-221 |
| 8CEN | EM | 3.0 Å | D=1-221 |
| 9KD7 | EM | 3.09 Å | D=1-221 |
| 7ML4 | EM | 3.1 Å | D=1-221 |
| 7ZS9 | EM | 3.1 Å | D=1-221 |
| 8TVY | EM | 3.1 Å | D=1-221 |
| 4BY7 | X-ray | 3.15 Å | D=1-221 |
Showing 20 of 123 experimental structures (best resolution first).
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