6O0X

Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9.

Zhu, X.Clarke, R.Puppala, A.K.Chittori, S.Merk, A.Merrill, B.J.Simonovic, M.Subramaniam, S.

(2019) Nat.Struct.Mol.Biol. 26: 679-685

  • DOI: 10.1038/s41594-019-0258-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RNA-guided Cas9 endonuclease from Streptococcus pyogenes is a single-turnover enzyme that displays a stable product state after double-stranded-DNA cleavage. Here, we present cryo-EM structures of precatalytic, postcatalytic and product states of ...

    The RNA-guided Cas9 endonuclease from Streptococcus pyogenes is a single-turnover enzyme that displays a stable product state after double-stranded-DNA cleavage. Here, we present cryo-EM structures of precatalytic, postcatalytic and product states of the active Cas9-sgRNA-DNA complex in the presence of Mg 2+ . In the precatalytic state, Cas9 adopts the 'checkpoint' conformation with the HNH nuclease domain positioned far away from the DNA. Transition to the postcatalytic state involves a dramatic ~34-Å swing of the HNH domain and disorder of the REC2 recognition domain. The postcatalytic state captures the cleaved substrate bound to the catalytically competent HNH active site. In the product state, the HNH domain is disordered, REC2 returns to the precatalytic conformation, and additional interactions of REC3 and RuvC with nucleic acids are formed. The coupled domain motions and interactions between the enzyme and the RNA-DNA hybrid provide new insights into the mechanism of genome editing by Cas9.


    Organizational Affiliation

    Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA. msimon5@uic.edu.,University of British Columbia, Vancouver, British Columbia, Canada. sriram.subramaniam@ubc.ca.,Frederick National Laboratory for Cancer Research, Frederick, MD, USA. sriram.subramaniam@ubc.ca.,Genome Editing Core, University of Illinois at Chicago, Chicago, IL, USA. merrillb@uic.edu.,University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA. merrillb@uic.edu.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas9/Csn1
A
1372Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: cas9 (csn1)
EC: 3.1.-.-
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99ZW2
Entity ID: 2
MoleculeChainsLengthOrganism
single guide RNAB102synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5' product of target strand DNAC13synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
non-target strand DNAD40synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
3' product of target strand DNAc27synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States097042
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human DevelopmentUnited States081534
National Institutes of Health/National Cancer InstituteUnited States--

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-24
    Type: Data collection, Database references
  • Version 1.2: 2019-08-21
    Type: Data collection, Database references