4QYZ | pdb_00004qyz

Crystal structure of a CRISPR RNA-guided surveillance complex, Cascade, bound to a ssDNA target

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 
    0.267 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target.

Mulepati, S., Heroux, A., Bailey, S.

(2014) Science 345: 1479-1484

  • DOI: https://doi.org/10.1126/science.1256996
  • Primary Citation of Related Structures:  
    4QYZ

  • PubMed Abstract: 

    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

    • Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasA502Escherichia 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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Go to UniProtKB:  Q46901
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UniProt GroupQ46901
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasB
B, C
160Escherichia coli K-12Mutation(s): 0 
Gene Names: casB, cse2, ygcK, b2759, JW2729
UniProt
Find proteins for P76632 (Escherichia coli (strain K12))
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UniProt GroupP76632
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasC
D, E, F, G, H
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasD224Escherichia 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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasE199Escherichia 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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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
N [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free:  0.267 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.869α = 90
b = 223.869β = 90
c = 290.651γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary