5F9R

Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.

Jiang, F.Taylor, D.W.Chen, J.S.Kornfeld, J.E.Zhou, K.Thompson, A.J.Nogales, E.Doudna, J.A.

(2016) Science 351: 867-871

  • DOI: 10.1126/science.aad8282

  • PubMed Abstract: 
  • Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand ...

    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas9/Csn1
B
1368Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: cas9 (csn1)
EC: 3.1.-.-
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99ZW2
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (116-MER)A118Streptococcus pyogenes MGAS8232
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (30-MER)C30Lambdapapillomavirus 1
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3')D30Lambdapapillomavirus 1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.237 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 147.940α = 90.00
b = 230.100β = 90.00
c = 417.650γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
PHENIXphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references
  • Version 1.2: 2016-03-09
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations