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Structure paper

TitleAcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 120, Issue 31, Page e2303675120, Year 2023
Publish dateJul 26, 2023
AuthorsWei Sun / Zhi Cheng / Jiuyu Wang / Jing Yang / Xueyan Li / Jinlong Wang / Minxuan Chen / Xiaoqi Yang / Gang Sheng / Jizhong Lou / Yanli Wang /
PubMed AbstractAnti-CRISPR (Acr) proteins are encoded by phages and other mobile genetic elements and inhibit host CRISPR-Cas immunity using versatile strategies. AcrIIC4 is a broad-spectrum Acr that inhibits the ...Anti-CRISPR (Acr) proteins are encoded by phages and other mobile genetic elements and inhibit host CRISPR-Cas immunity using versatile strategies. AcrIIC4 is a broad-spectrum Acr that inhibits the type II-C CRISPR-Cas9 system in several species by an unknown mechanism. Here, we determined a series of structures of Cas9 (HpaCas9)-sgRNA in complex with AcrIIC4 and/or target DNA, as well as the crystal structure of AcrIIC4 alone. We found that AcrIIC4 resides in the crevice between the REC1 and REC2 domains of HpaCas9, where its extensive interactions restrict the mobility of the REC2 domain and prevent the unwinding of target double-stranded (ds) DNA at the PAM-distal end. Therefore, the full-length guide RNA:target DNA heteroduplex fails to form in the presence of AcrIIC4, preventing Cas9 nuclease activation. Altogether, our structural and biochemical studies illuminate a unique Acr mechanism that allows DNA binding to the Cas9 effector complex but blocks its cleavage by preventing R-loop formation, a key step supporting DNA cleavage by Cas9.
External linksProc Natl Acad Sci U S A / PubMed:37494395 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.54 - 3.41 Å
Structure data

34919

8hnv

EMDB-34919, PDB-8hnv:
CryoEM structure of HpaCas9-sgRNA-dsDNA in the presence of AcrIIC4
Method: EM (single particle) / Resolution: 3.1 Å

PDB-8hns:
Crystal structure of an anti-CRISPR protein AcrIIC4 in apo form
Method: X-RAY DIFFRACTION / Resolution: 2.54 Å

PDB-8hnt:
Crystal structure of anti-CRISPR protein AcrIIC4 bound to HpaCas9-sgRNA surveillance complex
Method: X-RAY DIFFRACTION / Resolution: 3.06 Å

PDB-8hnw:
Crystal structure of HpaCas9-sgRNA surveillance complex bound to double-stranded DNA
Method: X-RAY DIFFRACTION / Resolution: 3.41 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-HOH:
WATER / Water

Source
  • haemophilus parainfluenzae (bacteria)
  • synthetic construct (others)
KeywordsANTIMICROBIAL PROTEIN / anti-CRISPR protein / cleavage inhibition / dimer / IMMUNE SYSTEM / Cas9 / REC lobe / HYDROLASE-RNA-ANTIMICROBIAL PROTEIN complex / dsDNA

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