Peptide chain release factor RF2 (prfB) is a 378-residue protein from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q5SM01.
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The mean pLDDT of this model is 81.7 (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 | 39% |
| 70 to 90 | Confident: backbone generally right | 47% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 9% |
What pLDDT means and how to read it
Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (Probable). In endogenous ribosomes interacts with P-site tRNA and 23S rRNA (PubMed:18988853, PubMed:20421507). In the presence of truncated mRNA in the 70S ribosome, ArfA and RF2 interact such that the GGQ peptide hydrolysis motif of RF2 rises into the peptidyl-transferase center and releases the ribosome (By similarity). Recruited to stalled E.coli 70S ribosomes by E.coli ArfA, but cannot be functionally accomodated in the peptidyl-transferase center (PubMed:27934701, PubMed:28077875). Note T.thermophilus probably does not encode arfA (Ref.1)
Interacts with the ribosome (PubMed:16377566, PubMed:17272297, PubMed:18988853, PubMed:20421507). Interacts with ribosomal protein L11 (PubMed:18988853). Recruited to stalled E.coli ribosomes by E.coli ArfA (PubMed:27934701, PubMed:28077875)
Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2IHR | X-ray | 2.5 Å | 1=27-378 |
| 4V67 | X-ray | 3.0 Å | AX/CX=1-378 |
| 4V5J | X-ray | 3.1 Å | AY/CY=28-369 |
| 6C5L | X-ray | 3.2 Å | AY/CY=28-369 |
| 5MDY | EM | 3.35 Å | 7=1-378 |
| 4V5E | X-ray | 3.45 Å | AY/CY=28-369 |
| 4V4S | X-ray | 6.76 Å | AY=20-378 |
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