DNA-directed RNA polymerase subunit alpha (rpoA) is a 329-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0A7Z4.
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The mean pLDDT of this model is 84.9 (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 | 50% |
| 70 to 90 | Confident: backbone generally right | 37% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme
Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription. Both the N- and C-terminus interact with different regions of transcriptional regulator CRP. The rRNA transcription and antitermination complex (rrnTAC) consists of RNAP, NusA, NusB, NusE (rpsJ),…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3K4G | X-ray | 2.05 Å | A/B/C/D/E/F/G/H=245-329 |
| 8FVW | EM | 2.1 Å | D/E=1-329 |
| 8FVR | EM | 2.42 Å | D/E=1-329 |
| 8HKC | EM | 2.49 Å | A/B=1-329 |
| 1BDF | X-ray | 2.5 Å | A/B/C/D=1-235 |
| 6XL5 | EM | 2.5 Å | A/B=1-329 |
| 6XL9 | EM | 2.5 Å | A/B=1-329 |
| 8F1J | EM | 2.6 Å | G/H=1-329 |
| 8PIB | EM | 2.6 Å | G/H=1-329 |
| 9MSF | EM | 2.6 Å | G/H=1-329 |
| 9YMV | EM | 2.6 Å | G/H=1-329 |
| 8SY7 | EM | 2.65 Å | A/G=1-329 |
| 6XLJ | EM | 2.7 Å | A/B=1-329 |
| 6XLL | EM | 2.7 Å | A/B=1-329 |
| 8SY5 | EM | 2.7 Å | A/G=1-329 |
| 9GDA | EM | 2.7 Å | A/B=1-329 |
| 9MSE | EM | 2.7 Å | G/H=1-329 |
| 9MSG | EM | 2.7 Å | G/H=1-329 |
| 9YMU | EM | 2.7 Å | G/H=1-329 |
| 9YMW | EM | 2.7 Å | G/H=1-329 |
Showing 20 of 382 experimental structures (best resolution first).
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