Crystal structure of T. fusca Cas3

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report

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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: https://doi.org/10.1038/nsmb.2875
  • Primary Citation of Related Structures:  
    4QQW, 4QQX, 4QQY, 4QQZ

  • 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, 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated helicase, Cas3 family
A, C, E, G
964Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_1593
Find proteins for Q47PJ0 (Thermobifida fusca (strain YX))
Explore Q47PJ0 
Go to UniProtKB:  Q47PJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47PJ0
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
B, D, F, H
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.789α = 90
b = 218.542β = 105
c = 123.749γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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