6JHW

Structure of anti-CRISPR AcrIIC3 and NmeCas9 HNH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Anti-CRISPR AcrIIC3 discriminates between Cas9 orthologs via targeting the variable surface of the HNH nuclease domain.

Kim, Y.Lee, S.J.Yoon, H.J.Kim, N.K.Lee, B.J.Suh, J.Y.

(2019) FEBS J 286: 4661-4674

  • DOI: 10.1111/febs.15037
  • Primary Citation of Related Structures:  
    6JHW, 6JHV

  • PubMed Abstract: 
  • Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems constitute the adaptive immunity of bacteria and archaea, degrading nucleic acids of invading phages and plasmids. In response, phages employ anti-CRISPR (Acr) proteins as ...

    Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems constitute the adaptive immunity of bacteria and archaea, degrading nucleic acids of invading phages and plasmids. In response, phages employ anti-CRISPR (Acr) proteins as a counterdefense mechanism to neutralize the host immunity. AcrIIC3 directly inhibits target DNA cleavage of type II-C Cas9 of Neisseria meningitidis. Here, we show that AcrIIC3 interacts with the HNH nuclease domain of N. meningitidis Cas9 to inhibit its nuclease activity in an allosteric manner. The crystal structure of the AcrIIC3-HNH complex reveals that AcrIIC3 binds opposite the active site on the HNH nuclease domain. AcrIIC3 employs a unique interface for HNH, allowing it to discriminate between Cas9 orthologs, which contrasts with the broad spectrum of Cas9 inhibition by AcrIIC1. Interface residues of HNH provide key electrostatic and hydrophobic interactions that determine the host specificity of AcrIIC3. Mutations that replace HNH interfaces of N. meningitidis Cas9 with those of Geobacillus stearothermophilus Cas9 or Campylobacter jejuni Cas9 significantly attenuate AcrIIC3 binding, illustrating that the divergent interaction surface confers the host specificity of AcrIIC3. Our study demonstrates that the variable sequences of binding interface can define the target specificity of Acr proteins, suggesting potential applications in Cas9 control for gene editing.


    Organizational Affiliation

    Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AcrIIC3AC117Neisseria meningitidisMutation(s): 0 
Gene Names: COH52_04855
Find proteins for A0A425B395 (Neisseria meningitidis)
Explore A0A425B395 
Go to UniProtKB:  A0A425B395
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9BD139Neisseria meningitidisMutation(s): 0 
Gene Names: cas9ERS040961_01379
EC: 3.1
Find proteins for A1IQ68 (Neisseria meningitidis serogroup A / serotype 4A (strain Z2491))
Explore A1IQ68 
Go to UniProtKB:  A1IQ68
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.821α = 90
b = 53.821β = 90
c = 163.363γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-18
    Changes: Database references