5DDJ

Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.361 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design.

Kotecha, A.Seago, J.Scott, K.Burman, A.Loureiro, S.Ren, J.Porta, C.Ginn, H.M.Jackson, T.Perez-Martin, E.Siebert, C.A.Paul, G.Huiskonen, J.T.Jones, I.M.Esnouf, R.M.Fry, E.E.Maree, F.F.Charleston, B.Stuart, D.I.

(2015) Nat.Struct.Mol.Biol. 22: 788-794

  • DOI: 10.1038/nsmb.3096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interact ...

    Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.


    Organizational Affiliation

    Pirbright Institute, Pirbright, UK.,Diamond Light Source, Didcot, UK.,Merck Sharp &Dohme Animal Health, Cologne, Germany.,Transboundary Animal Disease Programme, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, South Africa.,Division of Structural Biology, University of Oxford, Oxford, UK.,Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa.,Animal and Microbial Sciences, University of Reading, Reading, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Foot and mouth disease virus, VP1
1
211Foot-and-mouth disease virus - type OMutation(s): 0 
Find proteins for Q6PMW3 (Foot-and-mouth disease virus - type O)
Go to UniProtKB:  Q6PMW3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Foot and mouth disease virus, VP2
2
218Foot-and-mouth disease virus - type OMutation(s): 1 
Find proteins for Q6PMW3 (Foot-and-mouth disease virus - type O)
Go to UniProtKB:  Q6PMW3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Foot and mouth disease virus, VP3
3
220Foot-and-mouth disease virus - type OMutation(s): 0 
Find proteins for Q6PMW3 (Foot-and-mouth disease virus - type O)
Go to UniProtKB:  Q6PMW3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
4
85Foot-and-mouth disease virus - type OMutation(s): 0 
Find proteins for Q6PMW3 (Foot-and-mouth disease virus - type O)
Go to UniProtKB:  Q6PMW3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Work: 0.361 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 344.080α = 90.00
b = 344.080β = 90.00
c = 344.080γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom089755

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2015-10-14
    Type: Database references