9HV9 | pdb_00009hv9

Crystal structure of Fab34 complexed with a 7-mer peptide of FMDV VP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.229 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cattle antibodies identify a cross-serotype broadly neutralising foot-and-mouth disease virus epitope.

Bonnet-Di Placido, M.Duyvesteyn, H.M.E.Steyn, A.W.Hay, A.L.Porta, C.Valdez, K.R.Lokhman, E.Crossley, S.Hanson, K.Mwangi, W.N.Munir, D.Perez-Martin, E.Knowles, N.J.Burman, A.Yassin, A.A.Asfor, A.Faralla, C.Lam, K.J.McComb, R.Leifeld, C.Pietersz, K.King, D.P.van den Born, E.Duncan, S.K.Charleston, B.Fry, E.E.Ren, J.Stuart, D.I.Hammond, J.A.

(2026) NPJ Vaccines 

  • DOI: https://doi.org/10.1038/s41541-026-01427-7
  • Primary Citation Related Structures: 
    9HV1, 9HV2, 9HV8, 9HV9, 9HVA

  • PubMed Abstract: 

    Foot-and-mouth disease virus (FMDV) causes a devastating disease that threatens global food security. Vaccination is hindered by antigenic diversity across serotypes. To identify cross-serotype neutralising epitopes, we isolated 24 FMDV-specific antibodies from cattle sequentially vaccinated with antigens from four serotypes, of which three neutralised three vaccine strains. These three antibodies neutralised 21 and bound 59 additional topotypes across O, A, Asia 1, and C serotypes. Cryo-EM complexes of Fabs with FMD virus-like particles indicated all three recognise a common flexible epitope at the VP1 C-terminus, confirmed by binding competition. Crystallography and structural modelling revealed that a normally inaccessible surface of the hydrophobic VP1 C-terminal peptides inserts into a similar groove in all three antibodies. Comparison of neutralisation activity and integrin receptor blocking by whole antibodies, F(ab') 2 s, and Fabs suggests neutralisation is mediated by Fc steric hindrance of receptor binding. This cryptic, linear, and cross-serotype neutralising epitope may inform improved FMD vaccines.


  • Organizational Affiliation
    • The Pirbright Institute, Pirbright, Surrey, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
heavy chainA [auth H]238Bos taurusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
light chainB [auth L]213Bos taurusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1C [auth A]7Foot-and-mouth disease virusMutation(s): 0 
UniProt
Find proteins for P03305 (Foot-and-mouth disease virus serotype O)
Explore P03305 
Go to UniProtKB:  P03305
Entity Groups  
UniProt GroupP03305
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
Q [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth H]
E [auth H]
G [auth H]
H
J [auth L]
D [auth H],
E [auth H],
G [auth H],
H,
J [auth L],
K [auth L],
L,
O [auth L],
P [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth H],
M [auth L],
N [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth H]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.258α = 90
b = 40.679β = 94.45
c = 71.704γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/ 1
Wellcome TrustUnited Kingdom060208/Z/00/Z

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Database references
  • Version 1.2: 2026-04-15
    Changes: Database references