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: 3.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    5CD4

  • 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, short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense) ...

    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 bwiedenheft@gmail.com.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasEA, M199Escherichia coli K-12Mutation(s): 0 
Gene Names: casE, cas6e, ygcH, b2756, JW2726
EC: 3.1
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12))
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UniProt GroupQ46897
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasC
B, C, D, E, F, G, N, O, P, Q, R, S
B, C, D, E, F, G, N, O, P, Q, R, S
363Escherichia coli K-12Mutation(s): 0 
Gene Names: casC, cas4, cse4, ygcJ, b2758, JW2728
UniProt
Find proteins for Q46899 (Escherichia coli (strain K12))
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UniProt GroupQ46899
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasDH, T224Escherichia coli K-12Mutation(s): 0 
Gene Names: casD, cas5, ygcI, b2757, JW5844
UniProt
Find proteins for Q46898 (Escherichia coli (strain K12))
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UniProt GroupQ46898
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasAI, U502Escherichia coli K-12Mutation(s): 0 
Gene Names: casA, cse1, ygcL, b2760, JW2730
UniProt
Find proteins for Q46901 (Escherichia coli (strain K12))
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UniProt GroupQ46901
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasBJ, K, V, W165Escherichia coli K-12Mutation(s): 0 
Gene Names: casB, cse2, ygcK, b2759, JW2729
UniProt
Find proteins for P76632 (Escherichia coli (strain K12))
Explore P76632 
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UniProt GroupP76632
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Entity ID: 6
MoleculeChainsLengthOrganismImage
crRNAL, X61Escherichia coli K-12
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
Y [auth I],
Z [auth U]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.99α = 90
b = 244.8β = 90
c = 426.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108888
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: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2016-06-01
    Changes: Data collection
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence