5DDJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 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:  
    5AC9, 5ACA, 5D8A, 5DDJ

  • 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 interactions and are often unstable ...

    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

    Diamond Light Source, Didcot, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Foot and mouth disease virus, VP1A [auth 1]211Foot-and-mouth disease virus OMutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
UniProt
Find proteins for Q6PMW3 (Foot-and-mouth disease virus - type O)
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UniProt GroupQ6PMW3
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Foot and mouth disease virus, VP2B [auth 2]218Foot-and-mouth disease virus OMutation(s): 1 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Foot and mouth disease virus, VP3C [auth 3]220Foot-and-mouth disease virus OMutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinD [auth 4]85Foot-and-mouth disease virus OMutation(s): 0 
EC: 2.7.7.48 (UniProt), 3.4.22.28 (UniProt), 3.4.22.46 (UniProt), 3.6.1.15 (UniProt)
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Work: 0.361 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 344.08α = 90
b = 344.08β = 90
c = 344.08γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom089755

Revision History  (Full details and data files)

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