5XBL

Structure of nuclease in complex with associated protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.052 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein

Guo, M.Wang, S.Zhu, Y.Wang, S.Xiong, Z.Yang, J.Xu, Z.Huang, Z.

(2017) Nature 546: 436-439

  • DOI: 10.1038/nature22377

  • PubMed Abstract: 
  • CRISPR-Cas9 systems are bacterial adaptive immune systems that defend against infection by phages. Through the RNA-guided endonuclease activity of Cas9 they degrade double-stranded DNA with a protospacer adjacent motif (PAM) and sequences complementa ...

    CRISPR-Cas9 systems are bacterial adaptive immune systems that defend against infection by phages. Through the RNA-guided endonuclease activity of Cas9 they degrade double-stranded DNA with a protospacer adjacent motif (PAM) and sequences complementary to the guide RNA. Recently, two anti-CRISPR proteins (AcrIIA2 and AcrIIA4 from Listeria monocytogenes prophages) were identified, both of which inhibit Streptococcus pyogenes Cas9 (SpyCas9) and L. monocytogenes Cas9 activity in bacteria and human cells. However, the mechanism of AcrIIA2- or AcrIIA4-mediated Cas9 inhibition remains unknown. Here we report a crystal structure of SpyCas9 in complex with a single-guide RNA (sgRNA) and AcrIIA4. Our data show that AcrIIA2 and AcrIIA4 interact with SpyCas9 in a sgRNA-dependent manner. The structure reveals that AcrIIA4 inhibits SpyCas9 activity by structurally mimicking the PAM to occupy the PAM-interacting site in the PAM-interacting domain, thereby blocking recognition of double-stranded DNA substrates by SpyCas9. AcrIIA4 further inhibits the endonuclease activity of SpyCas9 by shielding its RuvC active site. Structural comparison reveals that formation of the AcrIIA4-binding site of SpyCas9 is induced by sgRNA binding. Our study reveals the mechanism of SpyCas9 inhibition by AcrIIA4, providing a structural basis for developing 'off-switch' tools for SpyCas9 to avoid unwanted genome edits within cells and tissues.


    Organizational Affiliation

    HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas9/Csn1
A
1368Streptococcus pyogenes serotype M1Gene Names: cas9 (csn1)
EC: 3.1.-.-
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99ZW2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Associated protein
D
87N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (98-MER)B98Streptococcus pyogenes
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.052 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 108.406α = 90.00
b = 69.756β = 105.73
c = 129.240γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Data collection, Database references