Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 82.30 kDa 
• Atom Count: 4424 
• Modelled Residue Count: 546 
• Deposited Residue Count: 720 
• Unique protein chains: 1

2CJQ

Bovine viral diarrhea virus CP7-R12 RNA-dependent RNA polymerase

• PDB DOI: 10.2210/pdb2CJQ/pdb

• Classification: TRANSFERASE
• Organism(s): Bovine viral diarrhea virus 1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-04-05 Released: 2006-07-19 
• Deposition Author(s): Choi, K.H., Gallei, A., Becher, P., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

The Structure of Bovine Viral Diarrhea Virus RNA-Dependent RNA Polymerase and its Amino-Terminal Domain.

Choi, K.H., Gallei, A., Becher, P., Rossmann, M.G.

(2006) Structure 14: 1107

• PubMed: 16843892 
• DOI: 10.1016/j.str.2006.05.020
• Primary Citation of Related Structures:  
  2CJQ


• PubMed Abstract: 
  

Viral RNA-dependent RNA polymerases (RdRp) differ from DNA-dependent RNA polymerases, DNA-dependent DNA polymerases, and reverse transcriptases in that RdRps contain "fingertips" consisting of several polypeptide strands in the fingers domain interacting with the thumb domain. The crystal structure of bovine viral diarrhea virus (BVDV) RdRp containing an Asn438 duplication shows that the "N-terminal domain," which occurs only in pestiviruses such as BVDV, interacts with the polymerase component of the same polypeptide chain. This contrasts with the domain swapping observed in the previously determined structure of the BVDV NADL strain RdRp. By comparison with the NADL structure and through the use of biochemical data, it is possible that the N-terminal domain, in conjunction with the fingertips, is required to bind and assist the translocation of the RNA template. The partial disorder of the loop containing the additional Asn438 residue may explain the low replication rate of the recombinant compared with the wild-type virus.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DIRECTED RNA POLYMERASE	A	720	Bovine viral diarrhea virus 1	Mutation(s): 0  EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.113 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q96662 (Bovine viral diarrhea virus (strain CP7)) Explore Q96662  Go to UniProtKB:  Q96662

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.244	α = 90
b = 106.244	β = 90
c = 55.387	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-05 
• Released Date: 2006-07-19 
Deposition Author(s): Choi, K.H., Gallei, A., Becher, P., Rossmann, M.G.

Revision History  

• Version 1.0: 2006-07-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance