1OOP

The Crystal Structure of Swine Vesicular Disease Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Swine Vesicular Disease Virus and Implications for Host Adaptation

Fry, E.E.Knowles, N.J.Newman, J.W.I.Wilsden, G.Rao, Z.King, A.M.Q.Stuart, D.I.

(2003) J Virol 77: 5475-5486

  • DOI: 10.1128/jvi.77.9.5475-5486.2003
  • Primary Citation of Related Structures:  
    1OOP

  • PubMed Abstract: 
  • Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry ...

    Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry. The 3.0-A crystal structure of strain UK/27/72 SVDV (highly virulent) reveals the expected similarity in core structure to those of other picornaviruses, showing most similarity to the closest available structure to CBV5, that of coxsackievirus B3 (CBV3). Features that help to cement together and rigidify the protein subunits are extended in this virus, perhaps explaining its extreme tolerance of environmental factors. Using the large number of capsid sequences available for both SVDV and CBV5, we have mapped the amino acid substitutions that may have occurred during the supposed adaptation of SVDV to a new host onto the structure of SVDV and a model of the SVDV/CAR complex generated by reference to the cryo-electron microscopy-visualized complex of CBV3 and CAR. The changes fall into three clusters as follows: one lines the fivefold pore, a second maps to the CAR-binding site and partially overlaps the site for decay accelerating factor (DAF) to bind to echovirus 7 (ECHO7), and the third lies close to the fivefold axis, where the low-density lipoprotein receptor binds to the minor group of rhinoviruses. Later changes in SVDV (post-1971) map to the first two clusters and may, by optimizing recognition of a pig CAR and/or DAF homologue, have improved the adaptation of the virus to pigs.


    Organizational Affiliation

    Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein VP1A283Swine vesicular disease virus (STRAIN UKG/27/72)Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P13900 (Swine vesicular disease virus (strain UKG/27/72))
Explore P13900 
Go to UniProtKB:  P13900
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein VP2B261Swine vesicular disease virus (STRAIN UKG/27/72)Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P13900 (Swine vesicular disease virus (strain UKG/27/72))
Explore P13900 
Go to UniProtKB:  P13900
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein VP3C238Swine vesicular disease virus (STRAIN UKG/27/72)Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P13900 (Swine vesicular disease virus (strain UKG/27/72))
Explore P13900 
Go to UniProtKB:  P13900
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein VP4D69Swine vesicular disease virus (STRAIN UKG/27/72)Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P13900 (Swine vesicular disease virus (strain UKG/27/72))
Explore P13900 
Go to UniProtKB:  P13900
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

Download Ideal Coordinates CCD File 
E [auth A]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
 Ligand Interaction
MYR
Query on MYR

Download Ideal Coordinates CCD File 
F [auth D]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.245 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 354.1α = 90
b = 371.7β = 90
c = 318.6γ = 90
Software Package:
Software NamePurpose
Adxvdata processing
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description