9ED9
SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State III - checkpoint)
Summary for 9ED9
| Entry DOI | 10.2210/pdb9ed9/pdb |
| Related | 9EAK 9EAL |
| EMDB information | 47941 |
| Descriptor | sgRNA, PAM-distal Target Strand, Non-target strand, ... (5 entities in total) |
| Functional Keywords | crispr-associated endonuclease, dna binding protein, dna binding protein-dna-rna complex, dna binding protein/dna/rna |
| Biological source | Streptococcus pyogenes More |
| Total number of polymer chains | 5 |
| Total formula weight | 223883.28 |
| Authors | Kiernan, K.A.,Taylor, D.W. (deposition date: 2024-11-16, release date: 2025-06-18, Last modification date: 2025-07-09) |
| Primary citation | Kiernan, K.A.,Taylor, D.W. Visualization of a multi-turnover Cas9 after product release. Nat Commun, 16:5681-5681, 2025 Cited by PubMed Abstract: While the most widely used CRISPR-Cas enzyme is the Cas9 endonuclease from Streptococcus pyogenes (Cas9), it exhibits single-turnover enzyme kinetics which leads to long residence times on product DNA. This blocks access to DNA repair machinery and acts as a major bottleneck during CRISPR-Cas9 gene editing. Cas9 can eventually be removed from the product by extrinsic factors, such as translocating polymerases, but the mechanisms contributing to Cas9 dissociation following cleavage remain poorly understood. Here, we employ truncated guide RNAs as a strategy to weaken PAM-distal nucleic acid interactions and promote faster enzyme turnover. Using kinetics-guided cryo-EM, we examine the conformational landscape of a multi-turnover Cas9, including the first detailed snapshots of Cas9 dissociating from product DNA. We discovered that while the PAM-distal product dissociates from Cas9 following cleavage, tight binding of the PAM-proximal product directly inhibits re-binding of new targets. Our work provides direct evidence as to why Cas9 acts as a single-turnover enzyme and will guide future Cas9 engineering efforts. PubMed: 40593576DOI: 10.1038/s41467-025-60668-7 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.95 Å) |
Structure validation
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