An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3

Nat Struct Mol Biol. 2011 Jun;18(6):680-7. doi: 10.1038/nsmb.2043. Epub 2011 May 15.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Catalytic Domain
  • Crystallography, X-Ray
  • Endoribonucleases / chemistry*
  • Endoribonucleases / metabolism*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Structure, Tertiary
  • RNA / chemistry*
  • RNA / metabolism*
  • Thermus thermophilus / chemistry
  • Thermus thermophilus / enzymology*


  • RNA
  • Endoribonucleases

Associated data

  • PDB/2Y8W
  • PDB/2Y8Y
  • PDB/2Y9H