Alternative ribosome-rescue factor A (arfA) is a 72-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P36675.
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The mean pLDDT of this model is 81.3 (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 | 6% |
| 50 to 70 | Low: treat with caution | 35% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Rescues ribosomes stalled at the 3' end of non-stop mRNAs (PubMed:21062370, PubMed:21435036). This activity is crucial when the stalled ribosome cannot be rescued by the SsrA(tmRNA)-SmpB quality control system (PubMed:21062370, PubMed:21435036). Binds the 30S subunit, contacting 16S rRNA with the N-terminus near the decoding center and its C-terminus in the mRNA entry channel; contacts change in the presence of release factor 2 (RF2, also named PrfB) (PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Requires RF2/PrfB to hydrolyze stalled peptidyl-tRNA on the ribosome; recruits and probably helps position RF2/PrfB correctly in the ribosomal A site so…
Interacts with the 50S ribosomal subunit (PubMed:21062370, PubMed:25355516, PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Interacts with RF2/PrfB on the ribosome (PubMed:27906160, PubMed:27906161, PubMed:27934701, PubMed:28077875). Contacts ribosomal protein S12 (rpsL) (PubMed:27906160, PubMed:27906161)
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5MDV | EM | 2.97 Å | 6=1-60 |
| 5H5U | EM | 3.0 Å | 3=1-72 |
| 5MDW | EM | 3.06 Å | 6=1-60 |
| 5MGP | EM | 3.1 Å | w=2-46 |
| 5U9F | EM | 3.2 Å | Y=1-72 |
| 5U9G | EM | 3.2 Å | Y=1-72 |
| 6C4I | EM | 3.24 Å | w=1-55 |
| 5MDY | EM | 3.35 Å | 6=1-60 |
| 5U4I | EM | 3.5 Å | w=1-55 |
| 7OJ0 | EM | 3.5 Å | 6=1-46 |
| 5U4J | EM | 3.7 Å | w=1-55 |
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