8JA0 | pdb_00008ja0

Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibitory mechanism of CRISPR-Cas9 by AcrIIC4.

Li, X.Liao, F.Gao, J.Song, G.Zhang, C.Ji, N.Wang, X.Wen, J.He, J.Wei, Y.Zhang, H.Li, Z.Yu, G.Yin, H.

(2023) Nucleic Acids Res 51: 9442-9451

  • DOI: https://doi.org/10.1093/nar/gkad669
  • Primary Citation of Related Structures:  
    7XVQ, 8JA0

  • PubMed Abstract: 

    CRISPR-Cas systems act as the adaptive immune systems of bacteria and archaea, targeting and destroying invading foreign mobile genetic elements (MGEs) such as phages. MGEs have also evolved anti-CRISPR (Acr) proteins to inactivate the CRISPR-Cas systems. Recently, AcrIIC4, identified from Haemophilus parainfluenzae phage, has been reported to inhibit the endonuclease activity of Cas9 from Neisseria meningitidis (NmeCas9), but the inhibition mechanism is not clear. Here, we biochemically and structurally investigated the anti-CRISPR activity of AcrIIC4. AcrIIC4 folds into a helix bundle composed of three helices, which associates with the REC lobe of NmeCas9 and sgRNA. The REC2 domain of NmeCas9 is locked by AcrIIC4, perturbing the conformational dynamics required for the target DNA binding and cleavage. Furthermore, mutation of the key residues in the AcrIIC4-NmeCas9 and AcrIIC4-sgRNA interfaces largely abolishes the inhibitory effects of AcrIIC4. Our study offers new insights into the mechanism of AcrIIC4-mediated suppression of NmeCas9 and provides guidelines for the design of regulatory tools for Cas9-based gene editing applications.


  • Organizational Affiliation
    • State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas91,082Neisseria meningitidisMutation(s): 0 
Gene Names: cas9NMV_1993
EC: 3.1
UniProt
Find proteins for C9X1G5 (Neisseria meningitidis serogroup C (strain 8013))
Explore C9X1G5 
Go to UniProtKB:  C9X1G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9X1G5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinB [auth D]88Haemophilus parainfluenzaeMutation(s): 0 
Gene Names: NCTC10672_00033NCTC10672_02354
UniProt
Find proteins for A0A377JKY9 (Haemophilus parainfluenzae)
Explore A0A377JKY9 
Go to UniProtKB:  A0A377JKY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A377JKY9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (117-MER)C [auth B]117Neisseria meningitidis
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection
  • Version 1.2: 2025-02-26
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-07-02
    Changes: Data collection