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 1.5 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: https://doi.org/10.1126/science.aao0679
  • Primary Citation of Related Structures:  
    5VVJ, 5VVK, 5VVL, 5WFE

  • 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 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

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1
A, B, C, D
305Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbTcas1b2755JW2725
EC: 3.1
UniProt
Find proteins for Q46896 (Escherichia coli (strain K12))
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Go to UniProtKB:  Q46896
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UniProt GroupQ46896
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas2
E, F
103Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbFcas2b2754JW5438
EC: 3.1
UniProt
Find proteins for P45956 (Escherichia coli (strain K12))
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Go to UniProtKB:  P45956
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UniProt GroupP45956
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Integration host factor subunit alpha99Escherichia coli S88Mutation(s): 0 
Gene Names: ihfAhimAECS88_1763
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12))
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UniProt GroupP0A6X7
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Integration host factor subunit beta94Escherichia coli S88Mutation(s): 0 
Gene Names: ihfBhimDECS88_0940
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
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UniProt GroupP0A6Y1
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (28-MER)28synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (45-MER)61synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (76-MER)95synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (61-MER)62synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX
MODEL REFINEMENTPHENIX

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2017-09-27
    Changes: Database references, Experimental preparation
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references