4OO8 | pdb_00004oo8

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

• PDB DOI: https://doi.org/10.2210/pdb4OO8/pdb
• NAKB: 4OO8

• Classification: Hydrolase/DNA/RNA
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-01-31 Released: 2014-02-26 
• Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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

• PubMed: 24529477 
• DOI: https://doi.org/10.1016/j.cell.2014.02.001
• Primary Citation Related Structures: 
  4OO8


• 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 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.

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Organizational Affiliation: 
• Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Biomolecular Characterization Team and CREST/JST, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: [e-mail].
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 395.17 kDa 
• Atom Count: 24,153 
• Modeled Residue Count: 2,702 
• Deposited Residue Count: 2,986 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	A, D	1,372	Streptococcus pyogenes serotype M1	Mutation(s): 4  Gene Names: cas9 EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1) Explore Q99ZW2  Go to UniProtKB:  Q99ZW2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (97-MER)	B, E	98	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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, F	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.713	α = 97.68
b = 105.694	β = 98.43
c = 126.817	γ = 100.31

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BSS	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Nishimasu, H., Ishitani, R., Nureki, O.

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
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description