4TVX | pdb_00004tvx

Crystal structure of the E. coli CRISPR RNA-guided surveillance complex, Cascade


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 
    0.268 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4TVX

This is version 1.9 of the entry. See complete history

Literature

Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli.

Jackson, R.N.Golden, S.M.van Erp, P.B.Carter, J.Westra, E.R.Brouns, S.J.van der Oost, J.Terwilliger, T.C.Read, R.J.Wiedenheft, B.

(2014) Science 345: 1473-1479

  • DOI: https://doi.org/10.1126/science.1256328
  • Primary Citation Related Structures: 
    4TVX

  • PubMed Abstract: 

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade. Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence. Conserved sequences on the 3' and 5' ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo-A-form configuration. The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.

Macromolecule Content 

  • Total Structure Weight: 804.32 kDa 
  • Atom Count: 53,269 
  • Modeled Residue Count: 6,807 
  • Deposited Residue Count: 6,988 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasBA [auth W],
B [auth V],
C [auth K],
D [auth J]
165Escherichia coli K-12Mutation(s): 0 
Gene Names: casBcse2ygcKb2759JW2729
UniProt
Find proteins for P76632 (Escherichia coli (strain K12))
Explore P76632 
Go to UniProtKB:  P76632
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76632
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasC363Escherichia coli K-12Mutation(s): 0 
Gene Names: casCcas4cse4ygcJb2758JW2728
UniProt
Find proteins for Q46899 (Escherichia coli (strain K12))
Explore Q46899 
Go to UniProtKB:  Q46899
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46899
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasEK [auth A],
T [auth M]
199Escherichia coli K-12Mutation(s): 0 
Gene Names: casEcas6eygcHb2756JW2726
EC: 3.1
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12))
Explore Q46897 
Go to UniProtKB:  Q46897
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46897
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasDL [auth H],
S [auth T]
224Escherichia coli K-12Mutation(s): 0 
Gene Names: casDcas5ygcIb2757JW5844
UniProt
Find proteins for Q46898 (Escherichia coli (strain K12))
Explore Q46898 
Go to UniProtKB:  Q46898
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46898
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasAW [auth U],
X [auth I]
502Escherichia coli K-12Mutation(s): 0 
Gene Names: casAcse1ygcLb2760JW2730
UniProt
Find proteins for Q46901 (Escherichia coli (strain K12))
Explore Q46901 
Go to UniProtKB:  Q46901
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46901
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
Escherichia coli strain ECOR44 cluster 1 CRISPR regionU [auth L],
V [auth X]
61Escherichia coli
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free:  0.268 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.851α = 90
b = 214.541β = 90
c = 217.383γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM103500
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108888
National Science Foundation (NSF, United States)United StatesEPS-110134
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32 GM108436

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Derived calculations, Other
  • Version 1.2: 2014-08-27
    Changes: Database references
  • Version 1.3: 2014-10-01
    Changes: Database references
  • Version 1.4: 2014-12-10
    Changes: Other
  • Version 1.5: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.6: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.7: 2022-03-23
    Changes: Author supporting evidence, Database references, Refinement description
  • Version 1.8: 2023-12-27
    Changes: Data collection
  • Version 1.9: 2024-10-23
    Changes: Structure summary