CRISPR-associated endoribonuclease Cas2 (ygbF) is a 94-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P45956.
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The mean pLDDT of this model is 96.2 (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 | 92% |
| 70 to 90 | Confident: backbone generally right | 9% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) (PubMed:21255106, PubMed:24793649, PubMed:24920831). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The Cas1-Cas2 complex is involved in CRISPR adaptation, the first stage of CRISPR immunity, being required for the addition/removal of CRISPR spacers at the leader end of the CRISPR locus (PubMed:24793649, PubMed:24920831, PubMed:25707795). The…
Homodimer (Ref.10). Part of the Cas1-Cas2 complex (PubMed:24793649, PubMed:24920831, PubMed:25707795, PubMed:26478180, PubMed:26503043, Ref.12). Forms a hexamer with 2 Cas1 dimers sandwiching a Cas2 dimer (PubMed:24793649). The DNA lies across a flat surface extending from 1 Cas1 dimer, across the Cas2 dimer and contacting the other Cas1 dimer. Only 1 Cas1 protein from each dimer is catalytic,…
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4MAK | X-ray | 1.1 Å | A/B=1-94 |
| 4P6I | X-ray | 2.3 Å | A/B=1-94 |
| 5DLJ | X-ray | 2.6 Å | E/F=1-78 |
| 4QDL | X-ray | 2.7 Å | E/F=1-94 |
| 5DQZ | X-ray | 2.7 Å | E/F=1-94 |
| 5VVK | X-ray | 2.9 Å | E/F=1-94 |
| 5DS5 | X-ray | 2.95 Å | E/F=1-94 |
| 5DQT | X-ray | 3.1 Å | E/F/M/N=1-94 |
| 5DS4 | X-ray | 3.2 Å | E/F=1-94 |
| 5VVL | X-ray | 3.31 Å | E/F=1-94 |
| 5DS6 | X-ray | 3.35 Å | E/F=1-94 |
| 5WFE | EM | 3.64 Å | E/F=1-94 |
| 5VVJ | X-ray | 3.89 Å | E/F=1-94 |
| 5DQU | X-ray | 4.5 Å | E/F=1-94 |
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