5XVN

E. far Cas1-Cas2/prespacer binary complex

  • Classification: IMMUNE SYSTEM
  • Organism(s): Enterococcus faecalis TX0027
  • Expression System: Escherichia coli

  • 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; National Institutes of Health/National Center for Research Resources; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nature24020
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas1
A, B, C, D, I, J, K, L
288Enterococcus faecalis TX0027Mutation(s): 0 
Gene Names: cas1
EC: 3.1.-.-
Find proteins for E6GPD7 (Enterococcus faecalis TX0027)
Go to UniProtKB:  E6GPD7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endoribonuclease Cas2
E, F, M, N
109Enterococcus faecalis TX0027Mutation(s): 0 
Gene Names: cas2
EC: 3.1.-.-
Find proteins for E6GPD6 (Enterococcus faecalis TX0027)
Go to UniProtKB:  E6GPD6
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (28-MER)G,H,O,P28Enterococcus faecalis TX0027
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
E, F, M, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 160.711α = 90.00
b = 160.711β = 90.00
c = 187.965γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41-GM103403
National Institutes of Health/National Center for Research ResourcesUnited StatesS10 RR029205
National Science Foundation (United States)United StatesDMR-1332208
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM-103485

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Author supporting evidence, Database references