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- EMDB-54263: Trispecific fab 49 with O1M 93C virus like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-54263
TitleTrispecific fab 49 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 49
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: To Be Published / Year: 2026
Title: Cattle antibodies identify a cross- serotype broadly neutralising foot-and- mouth disease virus epitope
Authors: Bonnet-Di Placido M / Duyvesteyn HME / Stuart DI / Fry EE / Ren J
History
DepositionJul 3, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54263.png

Downloads & links

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Map

FileDownload / File: emd_54263.map.gz / Format: CCP4 / Size: 347.6 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 450 pix.
= 419.4 Å		0.93 Å/pix.
x 450 pix.
= 419.4 Å		0.93 Å/pix.
x 450 pix.
= 419.4 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: 0.07
Minimum - Maximum-0.39061832 - 0.7532707
Average (Standard dev.)0.0065460512 (±0.042985056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 419.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54263_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_54263_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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 49

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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 49

SupramoleculeName: Antibody fragment 49 / 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 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
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: 39994
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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