3GPQ

Crystal structure of macro domain of Chikungunya virus in complex with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket

Malet, H.Coutard, B.Jamal, S.Dutartre, H.Papageorgiou, N.Neuvonen, M.Ahola, T.Forrester, N.Gould, E.A.Lafitte, D.Ferron, F.Lescar, J.Gorbalenya, A.E.de Lamballerie, X.Canard, B.

(2009) J Virol 83: 6534-6545

  • DOI: 10.1128/JVI.00189-09
  • Primary Citation of Related Structures:  
    3GPO, 3GPQ, 3GPG, 3GQO, 3GQE

  • PubMed Abstract: 
  • Macro domains (also called "X domains") constitute a protein module family present in all kingdoms of life, including viruses of the Coronaviridae and Togaviridae families. Crystal structures of the macro domain from the Chikungunya virus (an "Old World" alphavirus) and the Venezuelan equine encephalitis virus (a "New World" alphavirus) were determined at resolutions of 1 ...

    Macro domains (also called "X domains") constitute a protein module family present in all kingdoms of life, including viruses of the Coronaviridae and Togaviridae families. Crystal structures of the macro domain from the Chikungunya virus (an "Old World" alphavirus) and the Venezuelan equine encephalitis virus (a "New World" alphavirus) were determined at resolutions of 1.65 and 2.30 A, respectively. These domains are active as adenosine di-phosphoribose 1''-phosphate phosphatases. Both the Chikungunya and the Venezuelan equine encephalitis virus macro domains are ADP-ribose binding modules, as revealed by structural and functional analysis. A single aspartic acid conserved through all macro domains is responsible for the specific binding of the adenine base. Sequence-unspecific binding to long, negatively charged polymers such as poly(ADP-ribose), DNA, and RNA is observed and attributed to positively charged patches outside of the active site pocket, as judged by mutagenesis and binding studies. The crystal structure of the Chikungunya virus macro domain with an RNA trimer shows a binding mode utilizing the same adenine-binding pocket as ADP-ribose, but avoiding the ADP-ribose 1''-phosphate phosphatase active site. This leaves the AMP binding site as the sole common feature in all macro domains.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3A, B, C, D168Chikungunya virus strain S27-African prototypeMutation(s): 0 
Gene Names: nsP3
EC: 2.1.1 (UniProt), 2.7.7 (UniProt), 3.1.3.33 (UniProt), 3.4.22 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 3.1.3.84 (UniProt), 2.7.7.19 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype))
Explore Q8JUX6 
Go to UniProtKB:  Q8JUX6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*AP*A)-3')E, F3N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.260 
    • R-Value Work: 0.215 
    • R-Value Observed: 0.218 
    • Space Group: P 31
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 86.824α = 90
    b = 86.824β = 90
    c = 81.316γ = 120
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    ADSCdata collection

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2009-07-21
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Advisory, Refinement description, Version format compliance