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 1.4 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:  
    6O0X, 6O0Z, 6O0Y

  • 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 active Cas9-sgRNA-DNA complex in the presence of Mg 2+ ...

    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. sriram.subramaniam@ubc.ca.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas9/Csn1A1372Streptococcus pyogenesMutation(s): 0 
Gene Names: cas9csn1SPy_1046
EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Explore Q99ZW2 
Go to UniProtKB:  Q99ZW2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
single guide RNAB102synthetic construct
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5' product of target strand DNAC13synthetic construct
    Protein Feature View
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    • Reference Sequence
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    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    non-target strand DNAD40synthetic construct
    Protein Feature View
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    • Reference Sequence
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    3' product of target strand DNAE [auth c]27synthetic construct
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

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

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States097042
    National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States081534
    National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

    Revision History  (Full details and data files)

    • Version 1.0: 2019-07-10
      Type: Initial release
    • Version 1.1: 2019-07-24
      Changes: Data collection, Database references
    • Version 1.2: 2019-08-21
      Changes: Data collection, Database references
    • Version 1.3: 2019-12-04
      Changes: Author supporting evidence
    • Version 1.4: 2019-12-18
      Changes: Other