DNA-directed RNA polymerase II subunit RPB4 (POLR2D) is a 142-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O15514.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 91.3 (very high 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 | 84% |
| 70 to 90 | Confident: backbone generally right | 8% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 4% |
What pLDDT means and how to read it
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. 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. POLR2D/RPB4 is part of a subcomplex with POLR2G/RPB7 that binds to a pocket formed by POLR2A/RPB1, POLR2B/RPB2 and POLR2F/RPABC2 at the base of the clamp element. The POLR2D/RPB4-POLR2G/RPB7 subcomplex seems to lock the clamp via POLR2G/RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft.…
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
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9EHZ | EM | 2.6 Å | D=1-142 |
| 2C35 | X-ray | 2.7 Å | A/C/E/G=1-142 |
| 8XSO | EM | 2.7 Å | D=1-142 |
| 8XRM | EM | 3.13 Å | D=1-142 |
| 9EI1 | EM | 3.2 Å | D=1-142 |
| 9EI3 | EM | 3.2 Å | D=1-142 |
| 8XRJ | EM | 3.6 Å | D=1-142 |
| 9EI4 | EM | 3.7 Å | D=1-142 |
| 5IYB | EM | 3.9 Å | D=1-142 |
| 5IYC | EM | 3.9 Å | D=1-142 |
| 5IYD | EM | 3.9 Å | D=1-142 |
| 6DRD | EM | 3.9 Å | D=1-142 |
| 8XVS | EM | 4.1 Å | D=1-142 |
| 6XRE | EM | 4.6 Å | D=1-142 |
| 9VD9 | EM | 4.6 Å | l=1-142 |
| 7LBM | EM | 4.8 Å | D=1-142 |
| 5IYA | EM | 5.4 Å | D=1-142 |
| 5IY9 | EM | 6.3 Å | D=1-142 |
| 5IY6 | EM | 7.2 Å | D=1-142 |
| 6O9L | EM | 7.2 Å | D=1-142 |
Showing 20 of 22 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.