1WNE | pdb_00001wne

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

• PDB DOI: https://doi.org/10.2210/pdb1WNE/pdb
• NAKB: 1WNE

• Classification: TRANSFERASE/RNA
• Organism(s): Foot-and-mouth disease virus C-S8c1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-07-31 Released: 2004-08-31 
• Deposition Author(s): Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmis, C., Domingo, E., Verdaguer, N.

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Experimental Data Snapshot

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

Starting Model: experimental

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 Biological Chem 279: 47212-47221

• PubMed: 15294895 
• DOI: https://doi.org/10.1074/jbc.M405465200
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.61 kDa 
• Atom Count: 3,997 
• Modeled Residue Count: 489 
• Deposited Residue Count: 489 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent RNA polymerase	C [auth A]	476	Foot-and-mouth disease virus C-S8c1	Mutation(s): 0  Gene Names: Viruses EC: 2.7.7.48
UniProt
Find proteins for Q9QCE4 (Foot and mouth disease virus C) Explore Q9QCE4  Go to UniProtKB:  Q9QCE4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*AP*UP*GP*GP*GP*CP*C)-3'	A [auth B]	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*CP*C)-3'	B [auth C]	5	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.627	α = 90
b = 94.627	β = 90
c = 100.513	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-31 
Deposition Author(s): Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmis, C., Domingo, E., Verdaguer, N.

Revision History  

• 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
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description