4Q2C

Crystal structure of CRISPR-associated protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3

Gong, B.Shin, M.Sun, J.Jung, C.H.Bolt, E.L.van der Oost, J.Kim, J.-S.

(2014) Proc.Natl.Acad.Sci.USA --: --

  • DOI: 10.1073/pnas.1410806111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to ...

    Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.


    Organizational Affiliation

    Interdisciplinary Graduate Program in Molecular Medicine, Chonnam National University, Gwangju 501-746, Korea; Department of Chemistry, Chonnam National University, Gwangju 500-757, Korea;,School of Life Sciences, University of Nottingham Medical School, Nottingham NG72UH, United Kingdom; and.,Interdisciplinary Graduate Program in Molecular Medicine, Chonnam National University, Gwangju 501-746, Korea; Department of Chemistry, Chonnam National University, Gwangju 500-757, Korea; jsunkim@chonnam.ac.kr.,Department of Chemistry, Chonnam National University, Gwangju 500-757, Korea;,Laboratory of Microbiology, Wageningen University, 6703 HB, Wageningen, The Netherlands.,Interdisciplinary Graduate Program in Molecular Medicine, Chonnam National University, Gwangju 501-746, Korea;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated helicase Cas3
A
949Thermobaculum terrenum (strain ATCC BAA-798 / YNP1)Mutation(s): 0 
Find proteins for D1CGD0 (Thermobaculum terrenum (strain ATCC BAA-798 / YNP1))
Go to UniProtKB:  D1CGD0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 104.268α = 90.00
b = 214.558β = 90.00
c = 102.196γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release