5VW1

Crystal structure of SpyCas9-sgRNA-AcrIIA4 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9.

Yang, H.Patel, D.J.

(2017) Mol. Cell 67: 117-127.e5

  • DOI: 10.1016/j.molcel.2017.05.024

  • PubMed Abstract: 
  • Prokaryotic CRISPR-Cas adaptive immune systems utilize sequence-specific RNA-guided endonucleases to defend against infection by viruses, bacteriophages, and mobile elements, while these foreign genetic elements evolve diverse anti-CRISPR proteins to ...

    Prokaryotic CRISPR-Cas adaptive immune systems utilize sequence-specific RNA-guided endonucleases to defend against infection by viruses, bacteriophages, and mobile elements, while these foreign genetic elements evolve diverse anti-CRISPR proteins to overcome the CRISPR-Cas-mediated defense of the host. Recently, AcrIIA2 and AcrIIA4, encoded by Listeria monocytogene prophages, were shown to block the endonuclease activity of type II-A Streptococcus pyogene Cas9 (SpyCas9). We now report the crystal structure of AcrIIA4 in complex with single-guide RNA-bound SpyCas9, thereby establishing that AcrIIA4 preferentially targets critical residues essential for PAM duplex recognition, as well as blocks target DNA access to key catalytic residues lining the RuvC pocket. These structural insights, validated by biochemical assays on key mutants, demonstrate that AcrIIA4 competitively occupies both PAM-interacting and non-target DNA strand cleavage catalytic pockets. Our studies provide insights into anti-CRISPR-mediated suppression mechanisms for inactivating SpyCas9, thereby broadening the applicability of CRISPR-Cas regulatory tools for genome editing.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: yangh3@mskcc.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas9/Csn1
A
1370Streptococcus pyogenes serotype M1Gene Names: cas9 (csn1)
EC: 3.1.-.-
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99ZW2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
anti-CRISPR protein AcrIIA4
B
89N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
sgRNAC85Listeria monocytogenes
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.194α = 90.00
b = 101.242β = 90.00
c = 303.563γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-21 
  • Released Date: 2017-06-28 
  • Deposition Author(s): Yang, H., Patel, D.J.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM104962
Memorial Sloan Kettering Cancer Center Core GrantUnited StatesP30CA008748

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence