5FW1

Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9.

Anders, C.Bargsten, K.Jinek, M.

(2016) Mol Cell 61: 895

  • DOI: 10.1016/j.molcel.2016.02.020
  • Primary Citation of Related Structures:  
    5FW1, 5FW2, 5FW3

  • PubMed Abstract: 
  • The RNA-guided endonuclease Cas9 from Streptococcus pyogenes (SpCas9) forms the core of a powerful genome editing technology. DNA cleavage by SpCas9 is dependent on the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) in the target DNA, restricting the choice of targetable sequences ...

    The RNA-guided endonuclease Cas9 from Streptococcus pyogenes (SpCas9) forms the core of a powerful genome editing technology. DNA cleavage by SpCas9 is dependent on the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) in the target DNA, restricting the choice of targetable sequences. To address this limitation, artificial SpCas9 variants with altered PAM specificities have recently been developed. Here we report crystal structures of the VQR, EQR, and VRER SpCas9 variants bound to target DNAs containing their preferred PAM sequences. The structures reveal that the non-canonical PAMs are recognized by an induced fit mechanism. Besides mediating sequence-specific base recognition, the amino acid substitutions introduced in the SpCas9 variants facilitate conformational remodeling of the PAM region of the bound DNA. Guided by the structural data, we engineered a SpCas9 variant that specifically recognizes NAAG PAMs. Taken together, these studies inform further development of Cas9-based genome editing tools.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. Electronic address: jinek@bioc.uzh.ch.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1B1372Streptococcus pyogenesMutation(s): 5 
EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Explore Q99ZW2 
Go to UniProtKB:  Q99ZW2
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SGRNAA83synthetic construct
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
TARGET DNA STRANDC28synthetic construct
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  • Reference Sequence
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    NON-TARGET DNA STRANDD12synthetic construct
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    K
    Query on K

    Download Ideal Coordinates CCD File 
    E [auth A] , F [auth A] , I [auth B] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , 
    E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth D]
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    G [auth A], H [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.218 
    • R-Value Observed: 0.220 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 176.637α = 90
    b = 66.984β = 111.12
    c = 187.228γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    Aimlessdata scaling
    PHASERphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2016-04-20
      Type: Initial release
    • Version 2.0: 2019-10-23
      Changes: Atomic model, Data collection, Other