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- EMDB-54261: Trispecific fab 34 with O1M 93C virus like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-54261
TitleTrispecific fab 34 with O1M 93C virus like particle
Map data
Sample
  • Complex: Complex of trispecific fab-17 with stabilised O1M foot and mouth disease virus like particle
    • Complex: O1M Foot and Mouth disease virus like particle
    • Complex: Antibody fragment 34
KeywordsAntibody / cross reactive / FMDV / foot and mouth disease virus / neutralising / serotype / fab / VIRUS LIKE PARTICLE
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsStuart DI / Duyvesteyn HME / Ren J / Fry EE
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/ 1 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: NPJ Vaccines / Year: 2026
Title: Cattle antibodies identify a cross-serotype broadly neutralising foot-and-mouth disease virus epitope.
Authors: Marie Bonnet-Di Placido / Helen M E Duyvesteyn / Angela W Steyn / Abigail L Hay / Claudine Porta / Kristel Ramirez Valdez / Elena Lokhman / Sylvia Crossley / Kevan Hanson / William N Mwangi ...Authors: Marie Bonnet-Di Placido / Helen M E Duyvesteyn / Angela W Steyn / Abigail L Hay / Claudine Porta / Kristel Ramirez Valdez / Elena Lokhman / Sylvia Crossley / Kevan Hanson / William N Mwangi / Danish Munir / Eva Perez-Martin / Nick J Knowles / Alison Burman / Abdelaziz A Yassin / Amin Asfor / Cristina Faralla / Katherine J Lam / Róisín McComb / Carina Leifeld / Kimberly Pietersz / Donald P King / Erwin van den Born / Sherie K Duncan / Bryan Charleston / Elizabeth E Fry / Jingshan Ren / David I Stuart / John A Hammond /
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 ...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')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.
History
DepositionJul 3, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54261.png

Downloads & links

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Map

FileDownload / File: emd_54261.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 560 pix.
= 521.92 Å		0.93 Å/pix.
x 560 pix.
= 521.92 Å		0.93 Å/pix.
x 560 pix.
= 521.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0937
Minimum - Maximum-0.50936735 - 0.94894415
Average (Standard dev.)0.0032259864 (±0.03813635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 521.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54261_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54261_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of trispecific fab-17 with stabilised O1M foot and mouth ...

EntireName: Complex of trispecific fab-17 with stabilised O1M foot and mouth disease virus like particle
Components
  • Complex: Complex of trispecific fab-17 with stabilised O1M foot and mouth disease virus like particle
    • Complex: O1M Foot and Mouth disease virus like particle
    • Complex: Antibody fragment 34

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Supramolecule #1: Complex of trispecific fab-17 with stabilised O1M foot and mouth ...

SupramoleculeName: Complex of trispecific fab-17 with stabilised O1M foot and mouth disease virus like particle
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #2: O1M Foot and Mouth disease virus like particle

SupramoleculeName: O1M Foot and Mouth disease virus like particle / type: complex / ID: 2 / Parent: 1
Details: Expressed in baculovirus cells. Stabilising cysteine mutation.
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: Antibody fragment 34

SupramoleculeName: Antibody fragment 34 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Bos taurus (domestic cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: Harrick plasma
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio module in cryosparc
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 42467
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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