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TitleInsights into the compact CRISPR-Cas9d system.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2462, Year 2025
Publish dateMar 12, 2025
AuthorsJie Yang / Tongyao Wang / Ying Huang / Zhaoyi Long / Xuzichao Li / Shuqin Zhang / Lingling Zhang / Zhikun Liu / Qian Zhang / Huabing Sun / Minjie Zhang / Hang Yin / Zhongmin Liu / Heng Zhang /
PubMed AbstractCas9d, the smallest known member of the Cas9 family, employs a compact domain architecture for effective target cleavage. However, the underlying mechanism remains unclear. Here, we present the cryo- ...Cas9d, the smallest known member of the Cas9 family, employs a compact domain architecture for effective target cleavage. However, the underlying mechanism remains unclear. Here, we present the cryo-EM structures of the Cas9d-sgRNA complex in both target-free and target-bound states. Biochemical assays elucidated the PAM recognition and DNA cleavage mechanisms of Cas9d. Structural comparisons revealed that at least 17 base pairs in the guide-target heteroduplex is required for nuclease activity. Beyond its typical role as an adaptor between Cas9 enzymes and targets, the sgRNA also provides structural support and functional regulation for Cas9d. A segment of the sgRNA scaffold interacts with the REC domain to form a functional target recognition module. Upon target binding, this module undergoes a coordinated conformational rearrangement, enabling heteroduplex propagation and facilitating nuclease activity. This hybrid functional module precisely monitors heteroduplex complementarity, resulting in a lower mismatch tolerance compared to SpyCas9. Moreover, structure-guided engineering in both the sgRNA and Cas9d protein led to a more compact Cas9 system with well-maintained nuclease activity. Altogether, our findings provide insights into the target recognition and cleavage mechanisms of Cas9d and shed light on the development of high-fidelity mini-CRISPR tools.
External linksNat Commun / PubMed:40075056 / PubMed Central
MethodsEM (single particle)
Resolution2.65 - 2.87 Å
Structure data

60006

8zdr

EMDB-60006, PDB-8zdr:
Cryo-EM structure of the Cas9d-sgRNA-target DNA complex
Method: EM (single particle) / Resolution: 2.65 Å

60379

8zq9

EMDB-60379, PDB-8zq9:
Cryo-EM structure of the Cas9d-sgRNA complex
Method: EM (single particle) / Resolution: 2.87 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • metagenome (others)
KeywordsANTIVIRAL PROTEIN / a protein complex

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