4OO8

Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Cas9 in complex with guide RNA and target DNA

Nishimasu, H.Ran, F.A.Hsu, P.D.Konermann, S.Shehata, S.I.Dohmae, N.Ishitani, R.Zhang, F.Nureki, O.

(2014) Cell 156: 935-949

  • DOI: 10.1016/j.cell.2014.02.001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. The str ...

    The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly positioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the interaction with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan. Electronic address: nureki@biochem.s.u-tokyo.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas9/Csn1
A, D
1372Streptococcus pyogenes serotype M1Mutation(s): 4 
Gene Names: cas9csn1SPy_1046
EC: 3.1
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99ZW2

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
RNA (97-MER)B, E98N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3')C, F23N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.713α = 97.68
b = 105.694β = 98.43
c = 126.817γ = 100.31
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references