5DS6

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.352 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Foreign DNA capture during CRISPR-Cas adaptive immunity.

Nunez, J.K.Harrington, L.B.Kranzusch, P.J.Engelman, A.N.Doudna, J.A.

(2015) Nature 527: 535-538

  • DOI: 10.1038/nature15760
  • Primary Citation of Related Structures:  5DS4, 5DS5

  • PubMed Abstract: 
  • Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally ...

    Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally conserved Cas1-Cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. How the Cas1-Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1-Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas1
A, B, C, D
306Escherichia coli (strain K12)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
104Escherichia coli (strain K12)Gene Names: ygbF (cas2)
EC: 3.1.-.-
Find proteins for P45956 (Escherichia coli (strain K12))
Go to UniProtKB:  P45956
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (29-MER)G33Escherichia virus M13
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (28-MER)H33Escherichia virus M13
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.352 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.020α = 90.00
b = 123.006β = 90.00
c = 196.012γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2015-12-09
    Type: Database references
  • Version 1.3: 2016-04-06
    Type: Source and taxonomy