1WNE

Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with a template-primer RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Foot-and-Mouth Disease Virus RNA-dependent RNA Polymerase and Its Complex with a Template-Primer RNA

Ferrer-Orta, C.Arias, A.Perez-Luque, R.Escarmis, C.Domingo, E.Verdaguer, N.

(2004) J Biol Chem 279: 47212-47221

  • DOI: 10.1074/jbc.M405465200
  • Primary Citation of Related Structures:  
    1U09, 1WNE

  • PubMed Abstract: 
  • Genome replication in picornaviruses is catalyzed by a virally encoded RNA-dependent RNA polymerase, termed 3D. The enzyme performs this operation, together with other viral and probably host proteins, in the cytoplasm of their host cells. The crystal structure of the 3D polymerase of foot-and-mouth disease virus, one of the most important animal pathogens, has been determined unliganded and bound to a template-primer RNA decanucleotide ...

    Genome replication in picornaviruses is catalyzed by a virally encoded RNA-dependent RNA polymerase, termed 3D. The enzyme performs this operation, together with other viral and probably host proteins, in the cytoplasm of their host cells. The crystal structure of the 3D polymerase of foot-and-mouth disease virus, one of the most important animal pathogens, has been determined unliganded and bound to a template-primer RNA decanucleotide. The enzyme folds in the characteristic fingers, palm and thumb subdomains, with the presence of an NH2-terminal segment that encircles the active site. In the complex, several conserved amino acid side chains bind to the template-primer, likely mediating the initiation of RNA synthesis. The structure provides essential information for studies on RNA replication and the design of antiviral compounds.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, E-08028 Barcelona, Spain.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-dependent RNA polymeraseC [auth A]476Foot-and-mouth disease virus C-S8c1Mutation(s): 0 
Gene Names: Viruses
EC: 2.7.7.48 (PDB Primary Data), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
UniProt
Find proteins for Q9QCE4 (Foot-and-mouth disease virus - type C)
Explore Q9QCE4 
Go to UniProtKB:  Q9QCE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QCE4
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*CP*AP*UP*GP*GP*GP*CP*C)-3'A [auth B]8N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*CP*CP*C)-3'B [auth C]5N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.627α = 90
b = 94.627β = 90
c = 100.513γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance