2EC0

RNA-dependent RNA polymerase of foot-and-mouth disease virus in complex with a template-primer RNA and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

Starting Model: experimental
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This is version 1.3 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 U S A 104: 9463-9468

  • DOI: https://doi.org/10.1073/pnas.0700518104
  • Primary Citation of Related Structures:  
    2E9R, 2E9T, 2E9Z, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymeraseE [auth A],
F [auth D]
476Foot-and-mouth disease virus C-S8c1Mutation(s): 0 
Gene Names: 3D
EC: 2.7.7.48
UniProt
Find proteins for Q9QCE4 (Foot and mouth disease virus C)
Explore Q9QCE4 
Go to UniProtKB:  Q9QCE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QCE4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(P*AP*UP*GP*GP*GP*CP*CP*C)-3'A [auth B],
C [auth E]
8N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*GP*CP*CP*CP*A)-3'B [auth C],
D [auth F]
7N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.656α = 90
b = 95.656β = 90
c = 201.458γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ProDCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description