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.




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