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TitleStructural and functional bases of F. rodentium Cas9 provide insights into CRISPR-Cas protein engineering.
Journal, issue, pagesCell Genom, Vol. 6, Issue 1, Page 101039, Year 2026
Publish dateJan 14, 2026
AuthorsMei Yang / Siqi Liu / Guanqiao Chen / Xi Liu / Dapeng Sun / Jingjing Zhang / Yumei Wang / Shoudeng Chen / Rui Tian / Zheng Hu /
PubMed AbstractThe Faecalibaculum rodentium (Fr) CRISPR-Cas9 system exhibits enhanced gene-editing precision and efficiency compared to SpCas9, with distinctive advantages in targeting the TATA box in eukaryotic ...The Faecalibaculum rodentium (Fr) CRISPR-Cas9 system exhibits enhanced gene-editing precision and efficiency compared to SpCas9, with distinctive advantages in targeting the TATA box in eukaryotic promoters. However, the underlying molecular mechanisms remained unexplored. Here, we present cryo-electron microscopy structures of the FrCas9-single guide RNA (sgRNA)-DNA complex in both the R-loop expansion and pre-catalytic states, shedding light on its specialized recognition of the 5'-NRTA-3' protospacer adjacent motif (PAM) and the unusual overwinding of the sgRNA-DNA heteroduplex. Our investigations into the structure and extensive mutational analyses reveal that the phosphate lock loop plays a pivotal role in finely adjusting FrCas9's off-target sensitivity and catalytic efficiency. Remarkably, targeted residue substitutions in the phosphate lock loop and the PAM-distal region were found to synergistically enhance both the editing precision and efficiency of FrCas9. These findings advance our understanding of Cas9's accuracy and potency mechanisms while providing a molecular foundation for the rational design and development of next-generation CRISPR technologies.
External linksCell Genom / PubMed:41106392
MethodsEM (single particle)
Resolution2.89 - 3.46 Å
Structure data

61853

9jwk

EMDB-61853, PDB-9jwk:
Cryo-EM structure of FrCas9 in complex with sgRNA and 26-nt TS and 4-nt NTS substrates
Method: EM (single particle) / Resolution: 3.46 Å

61854

9jwn

EMDB-61854, PDB-9jwn:
Cryo-EM structure of FrCas9 in complex with sgRNA and 43-bp dsDNA substrate
Method: EM (single particle) / Resolution: 2.89 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • faecalibaculum rodentium (bacteria)
  • homo sapiens (human)
KeywordsHYDROLASE/RNA/DNA / FrCas9 / high fidelity / off-target / nuclease protein / complex / HYDROLASE / HYDROLASE-RNA-DNA complex / DNA/RNA/HYDROLASE / DNA-RNA-HYDROLASE complex

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