Crystal Structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea virus (BVDV)

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

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The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.

Choi, K.H.Groarke, J.M.Young, D.C.Kuhn, R.J.Smith, J.L.Pevear, D.C.Rossmann, M.G.

(2004) Proc Natl Acad Sci U S A 101: 4425-4430

  • DOI: https://doi.org/10.1073/pnas.0400660101
  • Primary Citation of Related Structures:  
    1S48, 1S49, 1S4F

  • PubMed Abstract: 

    The bovine viral diarrhea virus (BVDV) RNA-dependent RNA polymerase can initiate RNA replication by a de novo mechanism without a primer. The structure of BVDV polymerase, determined to 2.9-A resolution, contains a unique N-terminal domain, in addition to the fingers, palm, and thumb domains common to other polymerases. The structure of BVDV polymerase complexed with GTP, which is required for de novo (primer-independent) initiation, shows that GTP binds adjacent to the initiation NTP, suggesting that the GTP mimics a vestigial RNA product. Comparison of five monomers in two different crystal forms showed conformational changes in the fingertip region and in the thumb domain that may help to translocate the RNA template and product strands during elongation. The putative binding sites of previously reported BVDV inhibitors are also discussed.

  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase
A, B, C, D
601Bovine viral diarrhea virus 1Mutation(s): 0 
Find proteins for P19711 (Bovine viral diarrhea virus (isolate NADL))
Explore P19711 
Go to UniProtKB:  P19711
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19711
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 412.271α = 90
b = 412.271β = 90
c = 95.574γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance