4UN3

Crystal structure of Cas9 bound to PAM-containing DNA target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.593 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 

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:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
B
1372Streptococcus pyogenes serotype M1Mutation(s): 1 
Gene Names: cas9 (csn1)
EC: 3.1.-.-
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99ZW2
Entity ID: 1
MoleculeChainsLengthOrganism
SGRNAA83synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
TARGET DNA STRANDC28synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
NON-TARGET DNA STRANDD12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.593 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 177.723α = 90.00
b = 68.142β = 111.17
c = 188.230γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
autoSHARPphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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