Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

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

Macromolecule Content

• Total Structure Weight: 80.84 kDa 
• Atom Count: 5244 
• Modelled Residue Count: 665 
• Deposited Residue Count: 728 
• Unique protein chains: 4

5ACA

Structure-based energetics of protein interfaces guide Foot-and-Mouth disease virus vaccine design

• PDB DOI: 10.2210/pdb5ACA/pdb
• EM Map EMD-3130:EMDBEMDataResource

• Classification: VIRUS
• Organism(s): Foot-and-mouth disease virus SAT 2
• Expression System: Mesocricetus auratus
• Mutation(s): Yes 


• Deposited: 2015-08-14 Released: 2015-09-23 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-Based Energetics of Protein Interfaces Guide Foot-and-Mouth Disease 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

• PubMed: 26389739 
• 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. 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.

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Organizational Affiliation: 

Diamond Light Source, Didcot, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A [auth 1]	214	Foot-and-mouth disease virus SAT 2	Mutation(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 Q719N0 (Foot-and-mouth disease virus - type SAT 2) Explore Q719N0  Go to UniProtKB:  Q719N0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B [auth 2]	207	Foot-and-mouth disease virus SAT 2	Mutation(s): 1  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 Q719N0 (Foot-and-mouth disease virus - type SAT 2) Explore Q719N0  Go to UniProtKB:  Q719N0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C [auth 3]	222	Foot-and-mouth disease virus SAT 2	Mutation(s): 0
UniProt
Find proteins for Q1L764 (Foot-and-mouth disease virus - type SAT 2) Explore Q1L764  Go to UniProtKB:  Q1L764

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	D [auth 4]	85	Foot-and-mouth disease virus SAT 2	Mutation(s): 0
UniProt
Find proteins for Q1L764 (Foot-and-mouth disease virus - type SAT 2) Explore Q1L764  Go to UniProtKB:  Q1L764

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-14 
• Released Date: 2015-09-23 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2015-10-21
  Changes: Database references
• Version 1.3: 2017-08-30
  Changes: Data collection, Refinement description