4DOZ

Crystal structure of Pyrococcus furiosus Cmr2 (Cas10)

• PDB DOI: https://doi.org/10.2210/pdb4DOZ/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-12 Released: 2012-03-21 
• Deposition Author(s): Zhu, X., Ye, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.313 
• R-Value Work: 0.245 
• R-Value Observed: 0.248 

Literature

Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems

Zhu, X., Ye, K.

(2012) FEBS Lett 586: 939-945

• PubMed: 22449983 
• DOI: https://doi.org/10.1016/j.febslet.2012.02.036
• Primary Citation of Related Structures:  
  4DOZ


• PubMed Abstract: 
  

  CRISPR RNAs (crRNAs) mediate sequence-specific silencing of invading viruses and plasmids in prokaryotes. The crRNA-Cmr protein complex cleaves complementary RNA. We report the crystal structure of Pyrococcus furiosus Cmr2 (Cas10), a component of this Cmr complex and the signature protein in type III CRISPR systems. The structure reveals a nucleotide cyclase domain with a set of conserved catalytic residues that associates with an unexpected deviant cyclase domain like dimeric cyclases. Additionally, two helical domains resemble the thumb domain of A-family DNA polymerase and Cmr5, respectively. Our results suggest that Cmr2 possesses novel enzymatic activity that remains to be elucidated.

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Organizational Affiliation: 

College of Life Sciences, Beijing Normal University, Beijing 100875, China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 79.54 kDa 
• Atom Count: 4,522 
• Modelled Residue Count: 557 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	686	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF1129
UniProt
Find proteins for Q8U1S6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1S6  Go to UniProtKB:  Q8U1S6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.313 
• R-Value Work: 0.245 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.411	α = 90
b = 87.463	β = 90
c = 137.102	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Zhu, X., Ye, K.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations