9G6V | pdb_00009g6v

Dissociated FMDV SAT2 Pentamer in complex with ultralong Fab117


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A broadly reactive ultralong bovine antibody that can determine the integrity of foot-and-mouth disease virus capsids.

Clarke, J.D.Duyvesteyn, H.M.E.Perez-Martin, E.Latisenko, U.Porta, C.Humphreys, K.V.Hay, A.L.Ren, J.Fry, E.E.van den Born, E.Charleston, B.Bonnet-Di Placido, M.Owens, R.J.Stuart, D.I.Hammond, J.A.

(2024) J Gen Virol 105

  • DOI: https://doi.org/10.1099/jgv.0.002032
  • Primary Citation of Related Structures:  
    9G6V

  • PubMed Abstract: 

    Foot-and-mouth disease vaccination using inactivated virus is suboptimal, as the icosahedral viral capsids often disassemble into antigenically distinct pentameric units during long-term storage, or exposure to elevated temperature or lowered pH, and thus raise a response that is no longer protective. Furthermore, as foot-and-mouth disease virus (FMDV)'s seven serotypes are antigenically diverse, cross-protection from a single serotype vaccine is limited, and most existing mouse and bovine antibodies and camelid single-domain heavy chain-only antibodies are serotype-specific. For quality control purposes, there is a real need for pan-serotype antibodies that clearly distinguish between pentamer (12S) and protective intact FMDV capsid. To date, few cross-serotype bovine-derived antibodies have been reported in the literature. We identify a bovine antibody with an ultralong CDR-H3, Ab117, whose structural analysis reveals that it binds to a deep, hydrophobic pocket on the interior surface of the capsid via the CDR-H3. Main-chain and hydrophobic interactions provide broad serotype specificity. ELISA analysis confirms that Ab117 is a novel pan-serotype and conformational epitope-specific 12S reagent, suitable for assessing capsid integrity.


  • Organizational Affiliation

    The Division of Structural Biology, Nuffield Department of Medicine, The Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyproteinA [auth 1],
D [auth B],
F,
H [auth J],
J [auth N]
214Foot-and-mouth disease virus SAT 2Mutation(s): 0 
UniProt
Find proteins for Q719N0 (Foot-and-mouth disease virus serotype SAT-2)
Explore Q719N0 
Go to UniProtKB:  Q719N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ719N0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyproteinB [auth 2],
Q [auth C],
R [auth G],
S [auth K],
T [auth O]
219Foot-and-mouth disease virus SAT 2Mutation(s): 0 
UniProt
Find proteins for Q719N0 (Foot-and-mouth disease virus serotype SAT-2)
Explore Q719N0 
Go to UniProtKB:  Q719N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ719N0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyproteinC [auth 3],
E [auth D],
G [auth H],
I [auth L],
K [auth P]
222Foot-and-mouth disease virus SAT 2Mutation(s): 0 
UniProt
Find proteins for Q719N0 (Foot-and-mouth disease virus serotype SAT-2)
Explore Q719N0 
Go to UniProtKB:  Q719N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ719N0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab117 Heavy ChainL [auth A],
M [auth E],
N [auth I],
O [auth M],
P [auth Q]
308Bos taurusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011224/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom203141/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection
  • Version 1.2: 2024-11-20
    Changes: Data collection, Derived calculations, Other