5XVO

E. fae Cas1-Cas2/prespacer/target ternary complex revealing DNA sampling and half-integration states

  • Classification: IMMUNE SYSTEM
  • Organism(s): Enterococcus faecalis TX0027
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-06-28 Released: 2017-10-04 
  • Deposition Author(s): Xiao, Y., Ng, S., Nam, K.H., Ke, A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.

Xiao, Y.Ng, S.Hyun Nam, K.Ke, A.

(2017) Nature 550: 137-141

  • DOI: https://doi.org/10.1038/nature24020
  • Primary Citation of Related Structures:  
    5XVN, 5XVO, 5XVP

  • PubMed Abstract: 

    CRISPR (clustered regularly interspaced short palindromic repeats) and the nearby Cas (CRISPR-associated) operon establish an RNA-based adaptive immunity system in prokaryotes. Molecular memory is created when a short foreign DNA-derived prespacer is integrated into the CRISPR array as a new spacer. Whereas the RNA-guided CRISPR interference mechanism varies widely among CRISPR-Cas systems, the spacer integration mechanism is essentially identical. The conserved Cas1 and Cas2 proteins form an integrase complex consisting of two distal Cas1 dimers bridged by a Cas2 dimer. The prespacer is bound by Cas1-Cas2 as a dual-forked DNA, and the terminal 3'-OH of each 3' overhang serves as an attacking nucleophile during integration. The prespacer is preferentially integrated into the leader-proximal region of the CRISPR array, guided by the leader sequence and a pair of inverted repeats inside the CRISPR repeat. Spacer integration in the well-studied Escherichia coli type I-E CRISPR system also relies on the bacterial integration host factor. In type II-A CRISPR, however, Cas1-Cas2 alone integrates spacers efficiently in vitro; other Cas proteins (such as Cas9 and Csn2) have accessory roles in the biogenesis phase of prespacers. Here we present four structural snapshots from the type II-A system of Enterococcus faecalis Cas1 and Cas2 during spacer integration. Enterococcus faecalis Cas1-Cas2 selectively binds to a splayed 30-base-pair prespacer bearing 4-nucleotide 3' overhangs. Three molecular events take place upon encountering a target: first, the Cas1-Cas2-prespacer complex searches for half-sites stochastically, then it preferentially interacts with the leader-side CRISPR repeat, and finally, it catalyses a nucleophilic attack that connects one strand of the leader-proximal repeat to the prespacer 3' overhang. Recognition of the spacer half-site requires DNA bending and leads to full integration. We derive a mechanistic framework to explain the stepwise spacer integration process and the leader-proximal preference.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, New York 14853, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1
A, B, C, D, I
A, B, C, D, I, J, K, L
288Enterococcus faecalis TX0027Mutation(s): 0 
Gene Names: cas1HMPREF9501_02814
EC: 3.1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas2
E, F, M, N
109Enterococcus faecalis TX0027Mutation(s): 0 
Gene Names: cas2HMPREF9501_02813
EC: 3.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (28-MER)
G, O, P
28Enterococcus faecalis TX0027
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*GP*AP*G)-3')5Enterococcus faecalis TX0027
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (46-MER)46Enterococcus faecalis TX0027
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (69-MER)69Enterococcus faecalis TX0027
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.893α = 90
b = 124.8β = 106.5
c = 157.905γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXCDphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41-GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR029205
National Science Foundation (NSF, United States)United StatesDMR-1332208
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-103485

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2022-10-12
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection, Refinement description