5VGB

Crystal structure of NmeCas9 HNH domain bound to anti-CRISPR AcrIIC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Broad-Spectrum Inhibitor of CRISPR-Cas9.

Harrington, L.B.Doxzen, K.W.Ma, E.Liu, J.J.Knott, G.J.Edraki, A.Garcia, B.Amrani, N.Chen, J.S.Cofsky, J.C.Kranzusch, P.J.Sontheimer, E.J.Davidson, A.R.Maxwell, K.L.Doudna, J.A.

(2017) Cell 170: 1224-1233.e15

  • DOI: https://doi.org/10.1016/j.cell.2017.07.037
  • Primary Citation of Related Structures:  
    5VGB

  • PubMed Abstract: 

    CRISPR-Cas9 proteins function within bacterial immune systems to target and destroy invasive DNA and have been harnessed as a robust technology for genome editing. Small bacteriophage-encoded anti-CRISPR proteins (Acrs) can inactivate Cas9, providing an efficient off switch for Cas9-based applications. Here, we show that two Acrs, AcrIIC1 and AcrIIC3, inhibit Cas9 by distinct strategies. AcrIIC1 is a broad-spectrum Cas9 inhibitor that prevents DNA cutting by multiple divergent Cas9 orthologs through direct binding to the conserved HNH catalytic domain of Cas9. A crystal structure of an AcrIIC1-Cas9 HNH domain complex shows how AcrIIC1 traps Cas9 in a DNA-bound but catalytically inactive state. By contrast, AcrIIC3 blocks activity of a single Cas9 ortholog and induces Cas9 dimerization while preventing binding to the target DNA. These two orthogonal mechanisms allow for separate control of Cas9 target binding and cleavage and suggest applications to allow DNA binding while preventing DNA cutting by Cas9.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9142Neisseria meningitidisMutation(s): 0 
Gene Names: cas9NMA510612_0701
EC: 3.1
UniProt
Find proteins for X5EPV9 (Neisseria meningitidis)
Explore X5EPV9 
Go to UniProtKB:  X5EPV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5EPV9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-CRISPR protein (AcrIIC1)86Neisseria meningitidisMutation(s): 0 
UniProt
Find proteins for A0A2D0TCG3 (Neisseria meningitidis)
Explore A0A2D0TCG3 
Go to UniProtKB:  A0A2D0TCG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCG3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.164α = 90
b = 60.487β = 90
c = 77.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references