4UN3

Crystal structure of Cas9 bound to PAM-containing DNA target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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 ...

    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): 1 
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 STRANDC28synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    NON-TARGET DNA STRANDD12synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    A, B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.59 Å
    • R-Value Free: 0.252 
    • R-Value Work: 0.217 
    • R-Value Observed: 0.219 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 177.723α = 90
    b = 68.142β = 111.17
    c = 188.23γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    SCALAdata scaling
    autoSHARPphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • 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