4QYZ

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 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: casAcse1ygcLb2760JW2730
UniProt
Find proteins for Q46901 (Escherichia coli (strain K12))
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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: casBcse2ygcKb2759JW2729
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
D, E, F, G, H, I
363Escherichia coli K-12Mutation(s): 0 
Gene Names: casCcas4cse4ygcJb2758JW2728
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: casDcas5ygcIb2757JW5844
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: casEcas6eygcHb2756JW2726
EC: 3.1
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12))
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UniProt GroupQ46897
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (55-MER)61Escherichia coli
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (33-MER)40Lambdavirus lambda
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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 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • 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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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