2HCS

Crystal structure of RNA dependant RNA polymerase domain of West Nile virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5

Malet, H.Egloff, M.P.Selisko, B.Butcher, R.E.Wright, P.J.Roberts, M.Gruez, A.Sulzenbacher, G.Vonrhein, C.Bricogne, G.Mackenzie, J.M.Khromykh, A.A.Davidson, A.D.Canard, B.

(2007) J Biol Chem 282: 10678-10689

  • DOI: https://doi.org/10.1074/jbc.M607273200
  • Primary Citation of Related Structures:  
    2HCN, 2HCS, 2HFZ

  • PubMed Abstract: 

    Viruses of the family Flaviviridae are important human and animal pathogens. Among them, the Flaviviruses dengue (DENV) and West Nile (WNV) cause regular outbreaks with fatal outcomes. The RNA-dependent RNA polymerase (RdRp) activity of the non-structural protein 5 (NS5) is a key activity for viral RNA replication. In this study, crystal structures of enzymatically active and inactive WNV RdRp domains were determined at 3.0- and 2.35-A resolution, respectively. The determined structures were shown to be mostly similar to the RdRps of the Flaviviridae members hepatitis C and bovine viral diarrhea virus, although with unique elements characteristic for the WNV RdRp. Using a reverse genetic system, residues involved in putative interactions between the RNA-cap methyltransferase (MTase) and the RdRp domain of Flavivirus NS5 were identified. This allowed us to propose a model for the structure of the full-length WNV NS5 by in silico docking of the WNV MTase domain (modeled from our previously determined structure of the DENV MTase domain) onto the RdRp domain. The Flavivirus RdRp domain structure determined here should facilitate both the design of anti-Flavivirus drugs and structure-function studies of the Flavivirus replication complex in which the multifunctional NS5 protein plays a central role.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase (NS5)595Kunjin virusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P14335 (Kunjin virus (strain MRM61C))
Explore P14335 
Go to UniProtKB:  P14335
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14335
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.991α = 90
b = 109.991β = 90
c = 69.097γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
XPREPdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations