4UN4

Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease

Anders, C.Niewoehner, O.Duerst, A.Jinek, M.

(2014) Nature 513: 569

  • DOI: 10.1038/nature13579
  • Primary Citation of Related Structures:  
    4UN5, 4UN3, 4UN4

  • PubMed Abstract: 
  • The CRISPR-associated protein Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNA bearing sequences complementary to a 20-nucleotide segment in the guide RNA. Cas9 has emerged as a versatile molecular tool for genome editing and gene expression control ...

    The CRISPR-associated protein Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNA bearing sequences complementary to a 20-nucleotide segment in the guide RNA. Cas9 has emerged as a versatile molecular tool for genome editing and gene expression control. RNA-guided DNA recognition and cleavage strictly require the presence of a protospacer adjacent motif (PAM) in the target DNA. Here we report a crystal structure of Streptococcus pyogenes Cas9 in complex with a single-molecule guide RNA and a target DNA containing a canonical 5'-NGG-3' PAM. The structure reveals that the PAM motif resides in a base-paired DNA duplex. The non-complementary strand GG dinucleotide is read out via major-groove interactions with conserved arginine residues from the carboxy-terminal domain of Cas9. Interactions with the minor groove of the PAM duplex and the phosphodiester group at the +1 position in the target DNA strand contribute to local strand separation immediately upstream of the PAM. These observations suggest a mechanism for PAM-dependent target DNA melting and RNA-DNA hybrid formation. Furthermore, this study establishes a framework for the rational engineering of Cas9 enzymes with novel PAM specificities.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1B1372Streptococcus pyogenesMutation(s): 2 
EC: 3.1
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: 1
MoleculeChainsLengthOrganismImage
SGRNAA83synthetic construct
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    TARGET DNA STRAND PROXIMAL FRAGMENTC11synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      NON-TARGET DNA STRANDD11synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        TARGET DNA STRAND DISTAL FRAGMENTE17synthetic construct
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.37 Å
        • R-Value Free: 0.248 
        • R-Value Work: 0.217 
        • R-Value Observed: 0.218 
        • Space Group: C 1 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 177.78α = 90
        b = 66.816β = 111.39
        c = 186.834γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        XDSdata reduction
        SCALAdata scaling
        PHASERphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2014-07-23
          Type: Initial release
        • Version 1.1: 2014-08-13
          Changes: Database references
        • Version 1.2: 2014-10-01
          Changes: Database references