Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.12 kDa 
• Atom Count: 2345 
• Modelled Residue Count: 220 
• Deposited Residue Count: 234 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2Y8Y

Structure B of CRISPR endoribonuclease Cse3 bound to 19 nt RNA

• PDB DOI: 10.2210/pdb2Y8Y/pdb
• NDB: NA1113

• Classification: HYDROLASE/RNA
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-11 Released: 2011-05-18 
• Deposition Author(s): Sashital, D.G., Jinek, M., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.205 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Literature

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

• PubMed: 21572442 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CSE3	A	215	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: cse3, cas6, TTHB192 EC: 3.1
UniProt
Find proteins for Q53WG9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53WG9  Go to UniProtKB:  Q53WG9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*U)-3'	B	19	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 44.28	α = 90
b = 71.21	β = 90
c = 76.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-11 
• Released Date: 2011-05-18 
Deposition Author(s): Sashital, D.G., Jinek, M., Doudna, J.A.

Revision History  

• 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