3W2V

Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

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Literature

Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex.

Osawa, T.Inanaga, H.Numata, T.

(2013) J Mol Biol 425: 3811-3823

  • DOI: 10.1016/j.jmb.2013.03.042
  • Primary Citation of Related Structures:  
    3W2V, 3W2W

  • PubMed Abstract: 
  • Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci found in prokaryotes are transcribed to produce CRISPR RNAs (crRNAs) that, together with CRISPR-associated (Cas) proteins, target and degrade invading genetic materials. Cmr proteins (Cmr1-6) and crRNA form a sequence-specific RNA silencing effector complex ...

    Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci found in prokaryotes are transcribed to produce CRISPR RNAs (crRNAs) that, together with CRISPR-associated (Cas) proteins, target and degrade invading genetic materials. Cmr proteins (Cmr1-6) and crRNA form a sequence-specific RNA silencing effector complex. Here, we report the crystal structures of the Pyrococcus furiosus Cmr2-Cmr3 subcomplex bound with nucleotides (3'-AMP or ATP). The association of Cmr2 and Cmr3 forms an idiosyncratic crevasse, which binds the nucleotides. Cmr3 shares structural similarity with Cas6, which cleaves precursor crRNA for maturation, suggesting the divergent evolution of these proteins. Due to the structural resemblance, the properties of the RNA binding surface observed in Cas6 are well conserved in Cmr3, indicating the RNA binding ability of Cmr3. This surface of Cmr3 constitutes the crevasse observed in the Cmr2-Cmr3 complex. Our findings suggest that the Cmr2-Cmr3 complex uses the crevasse to bind crRNA and/or substrate RNA during the reaction.


    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cmr subunit Cmr2A677Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: cmr2PF1129
UniProt
Find proteins for Q8U1S6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1S6 
Go to UniProtKB:  Q8U1S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U1S6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cmr subunit Cmr3B322Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: cmr3PF1128
UniProt
Find proteins for Q8U1S7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U1S7 
Go to UniProtKB:  Q8U1S7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U1S7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AM
Query on 3AM

Download Ideal Coordinates CCD File 
D [auth A][(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate
C10 H14 N5 O7 P
LNQVTSROQXJCDD-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.94α = 90
b = 136.669β = 90
c = 191.973γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release