4CBG

Pestivirus NS3 helicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-Ray Structure of the Pestivirus Ns3 Helicase and its Conformation in Solution.

Tortorici, M.A.Duquerroy, S.Kwok, J.Vonrhein, C.Perez, J.Lamp, B.Bricogne, G.Rumenapf, T.Vachette, P.Rey, F.A.

(2015) J.Virol. 89: 4356

  • DOI: 10.1128/JVI.03165-14
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domai ...

    Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication.


    Organizational Affiliation

    Synchrotron Soleil, Gif sur Yvette, France.,Unité de Virologie Structurale, Département de Virologie, Institut Pasteur, Paris, France CNRS, UMR 3569, Paris, France tortoric@pasteur.fr rey@pasteur.fr.,Institute of Virology, University of Veterinary Medicine, Vienna, Austria.,Institut de Biologie Intégrative de la Cellule, UMR 9198, Gif-sur-Yvette, France.,Global Phasing Ltd., Cambridge, United Kingdom.,Unité de Virologie Structurale, Département de Virologie, Institut Pasteur, Paris, France CNRS, UMR 3569, Paris, France Université Paris Sud, Gif sur Yvette, France.,Unité de Virologie Structurale, Département de Virologie, Institut Pasteur, Paris, France Department of Physiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE NS3
A, B, C, D
516Classical swine fever virus (strain Alfort)Mutation(s): 0 
Find proteins for P19712 (Classical swine fever virus (strain Alfort))
Go to UniProtKB:  P19712
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.550α = 90.00
b = 168.360β = 98.52
c = 98.800γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2015-02-18
    Type: Database references
  • Version 1.3: 2015-04-15
    Type: Database references
  • Version 1.4: 2015-10-14
    Type: Refinement description