5CD4

The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli.

van Erp, P.B., Jackson, R.N., Carter, J., Golden, S.M., Bailey, S., Wiedenheft, B.

(2015) Nucleic Acids Res. 43: 8381-8391

  • DOI: 10.1093/nar/gkv793

  • PubMed Abstract: 

    • In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli ...

    In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli, short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 Å x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro. Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasE
A, M
199Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casE (cas6e, ygcH)
EC: 3.1.-.-
Find proteins for Q46897 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46897
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasC
B, C, D, E, F, G, N, O, P, Q, R, S
363Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casC (cas4, cse4, ygcJ)
Find proteins for Q46899 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46899
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasD
H, T
224Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casD (cas5, ygcI)
Find proteins for Q46898 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46898
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasA
I, U
502Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casA (cse1, ygcL)
Find proteins for Q46901 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46901
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasB
J, K, V, W
165Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: casB (cse2, ygcK)
Find proteins for P76632 (Escherichia coli (strain K12))
Go to UniProtKB:  P76632
Entity ID: 6
MoleculeChainsLengthOrganism
crRNAL,X61Escherichia coli K-12
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
I, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
23G
Query on 23G
L, X
RNA OH 3 prime terminusC10 H13 N5 O10 P2G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.990α = 90.00
b = 244.800β = 90.00
c = 426.740γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM108888
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32 GM108436

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2016-06-01
    Type: Data collection
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations