2E9Z

Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, ATP and UTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sequential structures provide insights into the fidelity of RNA replication

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

(2007) Proc.Natl.Acad.Sci.Usa 104: 9463-9468

  • DOI: 10.1073/pnas.0700518104
  • Primary Citation of Related Structures:  2E9R, 2E9T, 2EC0

  • PubMed Abstract: 
  • RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information c ...

    RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase
A
476Foot-and-mouth disease virus - type CN/A
Find proteins for Q9QCE4 (Foot-and-mouth disease virus - type C)
Go to UniProtKB:  Q9QCE4
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'B9N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*GP*GP*CP*CP*CP*A)-3'C7N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

Download SDF File 
Download CCD File 
A
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PPV
Query on PPV

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Download CCD File 
A
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.110α = 90.00
b = 94.110β = 90.00
c = 99.362γ = 120.00
Software Package:
Software NamePurpose
ProDCdata collection
REFMACrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance