5VVK

Cas1-Cas2 bound to full-site mimic

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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This is version 1.2 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) ...

    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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1
A, B, C, D
308Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbT, cas1, b2755, JW2725
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
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas2
E, F
94Escherichia coli K-12Mutation(s): 0 
Gene Names: ygbF, cas2, b2754, JW5438
EC: 3.1
UniProt
Find proteins for P45956 (Escherichia coli (strain K12))
Explore P45956 
Go to UniProtKB:  P45956
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UniProt GroupP45956
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*CP*CP*CP*AP*GP*TP*AP*GP*C)-3')11synthetic construct
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*CP*CP*AP*CP*CP*AP*GP*TP*G)-3')11synthetic construct
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (58-MER)I [auth J]58synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (58-MER)J [auth K]58synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.9α = 90
b = 197.612β = 112.7
c = 95.344γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1244557

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence