CRISPR-associated endonuclease Cas9/Csn1 (cas9) is a 1368-residue protein from Streptococcus pyogenes serotype M1. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q99ZW2.
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The mean pLDDT of this model is 88.4 (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 | 60% |
| 70 to 90 | Confident: backbone generally right | 34% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 1% |
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:21455174). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA; Cas9 only stabilizes the…
Monomer. Binds crRNA and tracrRNA
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8SCA | X-ray | 1.67 Å | B=497-713 |
| 6O56 | X-ray | 1.9 Å | A/B=775-908 |
| 5B2R | X-ray | 2.0 Å | B=1-1368 |
| 5FQ5 | X-ray | 2.14 Å | B=1-1368 |
| 7OXA | X-ray | 2.15 Å | B=1-1368 |
| 5B2S | X-ray | 2.2 Å | B=1-1368 |
| 5B2T | X-ray | 2.2 Å | B=1-1368 |
| 7QQV | X-ray | 2.25 Å | B=1-1368 |
| 7QQZ | X-ray | 2.25 Å | B=1-1368 |
| 7QR0 | X-ray | 2.3 Å | B=1-1368 |
| 4UN4 | X-ray | 2.37 Å | B=1-1368 |
| 4UN5 | X-ray | 2.4 Å | B=1-1368 |
| 7QQS | X-ray | 2.4 Å | B=1-1368 |
| 7QQX | X-ray | 2.4 Å | B=1-1368 |
| 7ZO1 | X-ray | 2.4 Å | B=1-1368 |
| 7OX9 | X-ray | 2.45 Å | B=1-1368 |
| 7QQU | X-ray | 2.45 Å | B=1-1368 |
| 4OO8 | X-ray | 2.5 Å | A/D=1-1368 |
| 5FW1 | X-ray | 2.5 Å | B=1-1368 |
| 7QQT | X-ray | 2.5 Å | B=1-1368 |
Showing 20 of 139 experimental structures (best resolution first).
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