RNA polymerase sigma factor RpoD (rpoD) is a 613-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P00579.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 83.2 (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 | 54% |
| 70 to 90 | Confident: backbone generally right | 30% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth. Preferentially transcribes genes associated with fast growth, such as ribosomal operons, other protein-synthesis related genes, rRNA- and tRNA-encoding genes and prfB
Interacts transiently with the RNA polymerase catalytic core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1 omega subunit) to form the RNA polymerase holoenzyme that can initiate transcription. Identified in a complex containing RpoD, the RNA polymerase subunits RpoA, RpoB and RpoZ, CRP and DNA. Interacts with Rsd; this prevents interaction with the RNA polymerase catalytic…
Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6XL5 | EM | 2.5 Å | F=1-613 |
| 6XL9 | EM | 2.5 Å | F=1-613 |
| 1SIG | X-ray | 2.6 Å | A=114-448 |
| 2P7V | X-ray | 2.6 Å | B=546-613 |
| 9YMV | EM | 2.6 Å | L=1-613 |
| 6XLJ | EM | 2.7 Å | F=1-613 |
| 6XLL | EM | 2.7 Å | F=1-613 |
| 9YMU | EM | 2.7 Å | L=1-613 |
| 9YMW | EM | 2.7 Å | L=1-613 |
| 9YMX | EM | 2.7 Å | L=1-613 |
| 8JO2 | EM | 2.74 Å | F=1-613 |
| 8FTD | EM | 2.76 Å | L=1-613 |
| 8TO1 | EM | 2.8 Å | L=1-613 |
| 7MKJ | EM | 2.9 Å | L=1-613 |
| 8TO6 | EM | 2.9 Å | L=1-613 |
| 8TO8 | EM | 2.9 Å | L=1-613 |
| 8TOE | EM | 2.9 Å | L=1-613 |
| 9YN0 | EM | 2.9 Å | L=1-613 |
| 7SZK | EM | 2.94 Å | F=1-613 |
| 6PST | EM | 3.0 Å | L=1-613 |
Showing 20 of 122 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.