5WFE

Cas1-Cas2-IHF-DNA holo-complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of the CRISPR genome integration complex.

Wright, A.V.Liu, J.J.Knott, G.J.Doxzen, K.W.Nogales, E.Doudna, J.A.

(2017) Science 357: 1113-1118

  • DOI: 10.1126/science.aao0679
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in inte ...

    CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo-electron microscopy structure of the full CRISPR locus integration complex, including the accessory protein IHF (integration host factor). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. These results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity.


    Organizational Affiliation

    Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. doudna@berkeley.edu.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas1
A, B, C, D
305Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ygbT (cas1)
EC: 3.1.-.-
Find proteins for Q46896 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46896
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endoribonuclease Cas2
E, F
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ygbF (cas2)
EC: 3.1.-.-
Find proteins for P45956 (Escherichia coli (strain K12))
Go to UniProtKB:  P45956
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Integration host factor subunit alpha
K
99Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: ihfA (himA)
Find proteins for B7MAS3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MAS3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Integration host factor subunit beta
L
94Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: ihfB (himD)
Find proteins for B7MHM1 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MHM1
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (28-MER)G28synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (45-MER)H61synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (76-MER)I95synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (61-MER)J62synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1244557
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1P50GM102706-01

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2017-09-27
    Type: Database references, Experimental preparation
  • Version 1.3: 2018-07-18
    Type: Data collection
  • Version 1.4: 2019-11-27
    Type: Author supporting evidence