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: 56.49 kDa 
• Atom Count: 4037 
• Modelled Residue Count: 487 
• Deposited Residue Count: 515 
• Unique protein chains: 1

2CKW

The 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.

• PDB DOI: 10.2210/pdb2CKW/pdb

• Classification: HYDROLASE
• Organism(s): Sapporo virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-04-24 Released: 2006-11-29 
• Deposition Author(s): Fullerton, S.W.B., Tucker, P.A., Rohayem, J., Coutard, B., Gebhardt, J., Gorbalenya, A., Canard, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

Literature

Structural and Functional Characterization of Sapovirus RNA-Dependent RNA Polymerase.

Fullerton, S.W.B., Blaschke, M., Coutard, B., Gebhardt, J., Gorbalenya, A., Canard, B., Tucker, P.A., Rohayem, J.

(2007) J Virol 81: 1858

• PubMed: 17121797 
• DOI: 10.1128/JVI.01462-06
• Primary Citation of Related Structures:  
  2CKW


• PubMed Abstract: 
  

Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D(pol)-like protein. Enzymatically active sapovirus 3D(pol) and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3D(pol) was determined by X-ray crystallography to 2.32-A resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D(pol) prefers Mn(2+) over Mg(2+) but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D(pol) synthesizes a double-stranded RNA or labels the template 3' terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D(pol) an attractive target for developing drugs to control calicivirus infection in humans.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Hamburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-DIRECTED RNA POLYMERASE	A	515	Sapporo virus	Mutation(s): 0  EC: 2.7.7.48 (PDB Primary Data), 3.6.1.15 (UniProt), 3.4.22.66 (UniProt)
UniProt
Find proteins for Q69014 (Sapporo virus (strain Human/United Kingdom/Manchester/1993)) Explore Q69014  Go to UniProtKB:  Q69014

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.434	α = 90
b = 93.881	β = 90
c = 94.771	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-24 
• Released Date: 2006-11-29 
Deposition Author(s): Fullerton, S.W.B., Tucker, P.A., Rohayem, J., Coutard, B., Gebhardt, J., Gorbalenya, A., Canard, B.

Revision History  

• Version 1.0: 2006-11-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2019-10-16
  Changes: Data collection, Other