4WFZ

Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase - NaCl Crystal Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structure-Function Relationships Underlying the Replication Fidelity of Viral RNA-Dependent RNA Polymerases.

Campagnola, G.McDonald, S.Beaucourt, S.Vignuzzi, M.Peersen, O.B.

(2015) J Virol 89: 275-286

  • DOI: 10.1128/JVI.01574-14
  • Primary Citation of Related Structures:  
    4WFX, 4WFY, 4WFZ

  • PubMed Abstract: 
  • Viral RNA-dependent RNA polymerases are considered to be low-fidelity enzymes, providing high mutation rates that allow for the rapid adaptation of RNA viruses to different host cell environments. Fidelity is tuned to provide the proper balance of virus replication rates, pathogenesis, and tissue tropism needed for virus growth ...

    Viral RNA-dependent RNA polymerases are considered to be low-fidelity enzymes, providing high mutation rates that allow for the rapid adaptation of RNA viruses to different host cell environments. Fidelity is tuned to provide the proper balance of virus replication rates, pathogenesis, and tissue tropism needed for virus growth. Using our structures of picornaviral polymerase-RNA elongation complexes, we have previously engineered more than a dozen coxsackievirus B3 polymerase mutations that significantly altered virus replication rates and in vivo fidelity and also provided a set of secondary adaptation mutations after tissue culture passage. Here we report a biochemical analysis of these mutations based on rapid stopped-flow kinetics to determine elongation rates and nucleotide discrimination factors. The data show a spatial separation of fidelity and replication rate effects within the polymerase structure. Mutations in the palm domain have the greatest effects on in vitro nucleotide discrimination, and these effects are strongly correlated with elongation rates and in vivo mutation frequencies, with faster polymerases having lower fidelity. Mutations located at the top of the finger domain, on the other hand, primarily affect elongation rates and have relatively minor effects on fidelity. Similar modulation effects are seen in poliovirus polymerase, an inherently lower-fidelity enzyme where analogous mutations increase nucleotide discrimination. These findings further our understanding of viral RNA-dependent RNA polymerase structure-function relationships and suggest that positive-strand RNA viruses retain a unique palm domain-based active-site closure mechanism to fine-tune replication fidelity.


    Organizational Affiliation

    Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA Olve.Peersen@ColoState.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA462Coxsackievirus B3 (strain Nancy)Mutation(s): 1 
EC: 2.7.7.48 (PDB Primary Data), 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt)
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy))
Explore P03313 
Go to UniProtKB:  P03313
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.423α = 90
b = 74.423β = 90
c = 288.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI059130

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2015-02-04
    Changes: Derived calculations
  • Version 1.4: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.5: 2017-11-22
    Changes: Refinement description
  • Version 1.6: 2019-12-11
    Changes: Author supporting evidence