5O6U

Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Variation of Type I-F CRISPR RNA Guided DNA Surveillance.

Pausch, P.Muller-Esparza, H.Gleditzsch, D.Altegoer, F.Randau, L.Bange, G.

(2017) Mol Cell 67: 622-632.e4

  • DOI: https://doi.org/10.1016/j.molcel.2017.06.036
  • Primary Citation of Related Structures:  
    5O6U, 5O7H

  • PubMed Abstract: 

    CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids. Type I CRISPR-Cas systems employ highly diverse, multi-subunit surveillance Cascade complexes that facilitate duplex formation between crRNA and complementary target DNA for R-loop formation, retention, and DNA degradation by the subsequently recruited nuclease Cas3. Typically, the large subunit recognizes bona fide targets through the PAM (protospacer adjacent motif), and the small subunit guides the non-target DNA strand. Here, we present the Apo- and target-DNA-bound structures of the I-Fv (type I-F variant) Cascade lacking the small and large subunits. Large and small subunits are functionally replaced by the 5' terminal crRNA cap Cas5fv and the backbone protein Cas7fv, respectively. Cas5fv facilitates PAM recognition from the DNA major groove site, in contrast to all other described type I systems. Comparison of the type I-Fv Cascade with an anti-CRISPR protein-bound I-F Cascade reveals that the type I-Fv structure differs substantially at known anti-CRISPR protein target sites and might therefore be resistant to viral Cascade interception.


  • Organizational Affiliation

    LOEWE Center for Synthetic Microbiology (Synmikro) and Faculty of Chemistry, Philipps-University-Marburg, Hans-Meerwein-Strasse C07, 35043 Marburg, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein, Csy4 family182Shewanella putrefaciens CN-32Mutation(s): 0 
Gene Names: Sputcn32_1823
UniProt
Find proteins for A4Y6G3 (Shewanella putrefaciens (strain CN-32 / ATCC BAA-453))
Explore A4Y6G3 
Go to UniProtKB:  A4Y6G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4Y6G3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
C, D, E
315Shewanella putrefaciens CN-32Mutation(s): 0 
Gene Names: Sputcn32_1821
UniProt
Find proteins for A4Y6G1 (Shewanella putrefaciens (strain CN-32 / ATCC BAA-453))
Explore A4Y6G1 
Go to UniProtKB:  A4Y6G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4Y6G1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein336Shewanella putrefaciens CN-32Mutation(s): 0 
Gene Names: Sputcn32_1822
UniProt
Find proteins for A4Y6G2 (Shewanella putrefaciens (strain CN-32 / ATCC BAA-453))
Explore A4Y6G2 
Go to UniProtKB:  A4Y6G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4Y6G2
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
crRNA43Shewanella putrefaciens CN-32
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains LengthOrganismImage
non-target DNAG [auth H]21Shewanella putrefaciens CN-32
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
target DNAH [auth I]27Shewanella putrefaciens CN-32
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.316α = 90
b = 143.316β = 90
c = 172.698γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations