4QQW

Crystal structure of T. fusca Cas3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.664 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation.

Huo, Y.Nam, K.H.Ding, F.Lee, H.Wu, L.Xiao, Y.Farchione, M.D.Zhou, S.Rajashankar, K.Kurinov, I.Zhang, R.Ke, A.

(2014) Nat.Struct.Mol.Biol. 21: 771-777

  • DOI: 10.1038/nsmb.2875
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CRISPR drives prokaryotic adaptation to invasive nucleic acids such as phages and plasmids, using an RNA-mediated interference mechanism. Interference in type I CRISPR-Cas systems requires a targeting Cascade complex and a degradation machine, Cas3, ...

    CRISPR drives prokaryotic adaptation to invasive nucleic acids such as phages and plasmids, using an RNA-mediated interference mechanism. Interference in type I CRISPR-Cas systems requires a targeting Cascade complex and a degradation machine, Cas3, which contains both nuclease and helicase activities. Here we report the crystal structures of Thermobifida fusca Cas3 bound to single-stranded (ss) DNA substrate and show that it is an obligate 3'-to-5' ssDNase that preferentially accepts substrate directly from the helicase moiety. Conserved residues in the HD-type nuclease coordinate two irons for ssDNA cleavage. We demonstrate ATP coordination and conformational flexibility of the SF2-type helicase domain. Cas3 is specifically guided toward Cascade-bound target DNA by a PAM sequence, through physical interactions with both the nontarget substrate strand and the CasA protein. The sequence of recognition events ensures well-controlled DNA targeting and degradation of foreign DNA by Cascade and Cas3.


    Organizational Affiliation

    Institute of Biochemistry and Cell Biology, Shanghai, China.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.,1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2] [3].,Howard Hughes Medical Institute, Mass Spectrometry Laboratory, University of California, Berkeley, Berkeley, California, USA.,Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, USA.,1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated helicase, Cas3 family
A, C, E, G
964Thermobifida fusca (strain YX)Mutation(s): 0 
Find proteins for Q47PJ0 (Thermobifida fusca (strain YX))
Go to UniProtKB:  Q47PJ0
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')B,D,F,H12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, C, E, G
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.664 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.789α = 90.00
b = 218.542β = 105.00
c = 123.749γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references