4QYZ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0303 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 

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: 10.1126/science.1256996

  • 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 struct ...

    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. scott.bailey@jhu.edu.,Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.,Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasA
A
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: 2
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasB
B, C
160Escherichia 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: 3
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasC
D, E, F, G, H, I
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: 4
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasD
J
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: 5
MoleculeChainsSequence LengthOrganismDetails
CRISPR system Cascade subunit CasE
K
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: 6
MoleculeChainsLengthOrganism
RNA (55-MER)L61Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (33-MER)M40Escherichia virus Lambda
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0303 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 223.869α = 90.00
b = 223.869β = 90.00
c = 290.651γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
Blu-Icedata collection
SOLVEphasing
XDSdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references