Structure B of CRISPR endoribonuclease Cse3 bound to 19 nt RNA

Experimental Data Snapshot

  • Resolution: 1.44 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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This is version 1.4 of the entry. See complete history


An RNA-Induced Conformational Change Required for Crispr RNA Cleavage by the Endoribonuclease Cse3.

Sashital, D.G.Jinek, M.Doudna, J.A.

(2011) Nat Struct Mol Biol 18: 680

  • DOI: https://doi.org/10.1038/nsmb.2043
  • Primary Citation of Related Structures:  
    2Y8W, 2Y8Y, 2Y9H

  • PubMed Abstract: 

    Clustered regularly interspaced short palindromic repeat (CRISPR) chromosomal loci found in prokaryotes provide an adaptive immune system against bacteriophages and plasmids. CRISPR-specific endoRNases produce short RNA molecules (crRNAs) from CRISPR transcripts, which harbor sequences complementary to invasive nucleic acid elements and ensure their selective targeting by CRISPR-associated (Cas) proteins. The extreme sequence divergence of CRISPR-specific endoRNases and their RNA substrates has obscured homology-based comparison of RNA recognition and cleavage mechanisms. Here, we show that Cse3 type CRISPR-specific endoRNases bind a hairpin structure and residues downstream of the cleavage site within the repetitive segment of cognate CRISPR RNA. Cocrystal structures of Cse3-RNA complexes reveal an RNA-induced conformational change in the enzyme active site that aligns the RNA strand for site-specific cleavage. These studies provide insight into a catalytically essential RNA recognition mechanism by a large class of CRISPR-related endoRNases.

  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CSE3215Thermus thermophilus HB8Mutation(s): 0 
Find proteins for Q53WG9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53WG9 
Go to UniProtKB:  Q53WG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53WG9
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.44 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.28α = 90
b = 71.21β = 90
c = 76.56γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-06-09
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-11-02
    Changes: Database references, Other
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description