4OGE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HNH endonuclease domain protein
A
1101Actinomyces naeslundii (strain ATCC 12104 / DSM 43013 / JCM 8349 / NCTC 10301 / Howell 279)Mutation(s): 0 
Gene Names: cas9
EC: 3.1.-.-
Find proteins for J3F2B0 (Actinomyces naeslundii (strain ATCC 12104 / DSM 43013 / JCM 8349 / NCTC 10301 / Howell 279))
Go to UniProtKB:  J3F2B0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

Download SDF File 
Download CCD File 
A
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.415α = 90.00
b = 133.025β = 96.22
c = 80.690γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SOLVEphasing
PHENIXrefinement
SCALAdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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