Pestivirus NS3 helicase

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1128/JVI.03165-14
  • Primary Citation of Related Structures:  
    4CBG, 4CBH, 4CBI, 4CBL, 4CBM

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
516Classical swine fever virusMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for P19712 (Classical swine fever virus (strain Alfort))
Explore P19712 
Go to UniProtKB:  P19712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19712
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.07α = 90
b = 144.44β = 92.94
c = 118.69γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2015-10-14
    Changes: Refinement description
  • Version 1.4: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description