4OGE

Crystal structure of the Type II-C Cas9 enzyme from Actinomyces naeslundii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.

Jinek, M.Jiang, F.Taylor, D.W.Sternberg, S.H.Kaya, E.Ma, E.Anders, C.Hauer, M.Zhou, K.Lin, S.Kaplan, M.Iavarone, A.T.Charpentier, E.Nogales, E.Doudna, J.A.

(2014) Science 343: 1247997-1247997

  • DOI: 10.1126/science.1247997
  • Primary Citation of Related Structures:  
    4CMP, 4CMQ, 4OGE, 4OGC

  • PubMed Abstract: 
  • Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 h ...

    Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HNH endonuclease domain proteinA1101Actinomyces naeslundii str. Howell 279Mutation(s): 0 
Gene Names: HMPREF1129_2620cas9
EC: 3.1
Find proteins for J3F2B0 (Actinomyces naeslundii (strain ATCC 12104 / DSM 43013 / JCM 8349 / NCTC 10301 / Howell 279))
Explore J3F2B0 
Go to UniProtKB:  J3F2B0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

Download CCD File 
A
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.415α = 90
b = 133.025β = 96.22
c = 80.69γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2014-03-26
    Changes: Database references