2JHA | pdb_00002jha

The structure of bluetongue virus VP4 reveals a multifunctional RNA- capping production-line

• PDB DOI: https://doi.org/10.2210/pdb2JHA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bluetongue virus (serotype 10 / American isolate)
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-02-21 Released: 2007-04-10 
• Deposition Author(s): Sutton, G., Grimes, J.M., Stuart, D.I., Roy, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.331 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Bluetongue Virus Vp4 is an RNA-Capping Assembly Line.

Sutton, G., Grimes, J.M., Stuart, D.I., Roy, P.

(2007) Nat Struct Mol Biol 14: 449

• PubMed: 17417654 
• DOI: https://doi.org/10.1038/nsmb1225
• Primary Citation Related Structures: 
  2JH8, 2JH9, 2JHA, 2JHC, 2JHP


• PubMed Abstract: 
  

  Eukaryotic organisms cap the 5' ends of their messenger RNAs by a series of four chemical reactions. Some viruses achieve this using a single molecule; the crystal structure of such an enzyme from bluetongue virus reveals an elongated modular architecture that provides a scaffold for an assemblage of active sites, two contributed by a domain of novel structure.

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Organizational Affiliation: 
• Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 76.59 kDa 
• Atom Count: 5,113 
• Modeled Residue Count: 613 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4 CORE PROTEIN	A	644	Bluetongue virus (serotype 10 / American isolate)	Mutation(s): 0
UniProt
Find proteins for P07132 (Bluetongue virus 10 (isolate USA)) Explore P07132  Go to UniProtKB:  P07132

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GP3	B [auth A]	DIGUANOSINE-5'-TRIPHOSPHATE C20 H27 N10 O18 P3 AAXYAFFKOSNMEB-MHARETSRSA-N
GUN	C [auth A], D [auth A]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.331 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.4	α = 90
b = 75.4	β = 90
c = 422.47	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Sutton, G., Grimes, J.M., Stuart, D.I., Roy, P.

Revision History  

• Version 1.0: 2007-04-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2015-09-23
  Changes: Source and taxonomy
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other