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- EMDB-55789: Structure of vaccine candidate AHSV-4 VP2 DI-mi3 nanoparticle -

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Basic information

Entry
Database: EMDB / ID: EMD-55789
TitleStructure of vaccine candidate AHSV-4 VP2 DI-mi3 nanoparticle
Map data
Sample
  • Complex: SC003-mi3 nanoparticles conjugated with AHSV-4 VP2 DI-SpyTag antigen
    • Complex: AHSV-4 VP2 DI domain antigen with SpyTag
    • Protein or peptide: DI-mi3 (conjugated nanoparticle)
KeywordsAHSV-4 VP2 DI domain / SpyTag/SpyCatcher system / MPSP / mi3 nanoparticles / antigen display / vaccine candidate / VIRUS LIKE PARTICLE
Biological speciesThermotoga maritima (bacteria) / African horse sickness virus 4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsMartinez-Castillo A / Aebischer A / Fu L / Breard E / Zientara S / Kortekaas J / Beer M / Abrescia NGA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)101059924European Union
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of African horse sickness virus VP2 receptor-binding protein enables nanoparticle vaccine design.
Authors: Ane Martínez-Castillo / Andrea Aebischer / Philippine Toneatti / Lifei Fu / Damien Vitour / Corinne Sailleau / Bernd Hoffmann / Kati Franzke / Michael Eschbaumer / Saskia Weber / Eva Calvo ...Authors: Ane Martínez-Castillo / Andrea Aebischer / Philippine Toneatti / Lifei Fu / Damien Vitour / Corinne Sailleau / Bernd Hoffmann / Kati Franzke / Michael Eschbaumer / Saskia Weber / Eva Calvo Pinilla / Javier Ortego / David Gil-Cartón / Emmanuel Bréard / Stéphan Zientara / Jeroen Kortekaas / Martin Beer / Nicola Ga Abrescia /
Abstract: African horse sickness virus (AHSV) is a lethal equine pathogen with no licensed vaccine other than vaccines containing attenuated virus, which pose safety risks. Endemic to sub-Saharan Africa, AHSV ...African horse sickness virus (AHSV) is a lethal equine pathogen with no licensed vaccine other than vaccines containing attenuated virus, which pose safety risks. Endemic to sub-Saharan Africa, AHSV has caused epizootics in Spain and Portugal, Cyprus, Morocco, the Middle East, India and Pakistan and, most recently, Thailand. Here, we resolve the 3.11 Å cryo-EM structure of full-length VP2 from AHSV serotype 4, adopting its native triskelion architecture and shedding light on an α-helical domain anchoring the triskelion core, which is absent in other structurally characterized orbiviruses. Structure-guided mapping identified a subdomain of VP2 as a key target of neutralizing antibodies. Displayed on nanoparticles using the SpyCatcher/SpyTag technology, the domain conferred complete protection from clinical disease after viral challenge infection in mice and elicited robust and long-lasting immune responses in horses, the target species of AHSV. These findings provide a structural blueprint for the next generation of recombinant vaccines against AHSV and related orbiviruses.
History
DepositionNov 21, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55789.png

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 256 pix.
= 421.888 Å		1.65 Å/pix.
x 256 pix.
= 421.888 Å		1.65 Å/pix.
x 256 pix.
= 421.888 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.409
Minimum - Maximum-1.8867424 - 2.7536292
Average (Standard dev.)0.010464663 (±0.11546982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 421.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55789_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_55789_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55789_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SC003-mi3 nanoparticles conjugated with AHSV-4 VP2 DI-SpyTag antigen

EntireName: SC003-mi3 nanoparticles conjugated with AHSV-4 VP2 DI-SpyTag antigen
Components
  • Complex: SC003-mi3 nanoparticles conjugated with AHSV-4 VP2 DI-SpyTag antigen
    • Complex: AHSV-4 VP2 DI domain antigen with SpyTag
    • Protein or peptide: DI-mi3 (conjugated nanoparticle)

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Supramolecule #1: SC003-mi3 nanoparticles conjugated with AHSV-4 VP2 DI-SpyTag antigen

SupramoleculeName: SC003-mi3 nanoparticles conjugated with AHSV-4 VP2 DI-SpyTag antigen
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermotoga maritima (bacteria)

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Supramolecule #2: AHSV-4 VP2 DI domain antigen with SpyTag

SupramoleculeName: AHSV-4 VP2 DI domain antigen with SpyTag / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: African horse sickness virus 4

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Macromolecule #1: DI-mi3 (conjugated nanoparticle)

MacromoleculeName: DI-mi3 (conjugated nanoparticle) / type: protein_or_peptide / ID: 1
Details: Please keep in mind that this sequence corresponds only to the SC-mi3 but the cryo-EM density refers to the SC-mi3 coupled to the DI antigen. Please see the article.
Enantiomer: DEXTRO
Source (natural)Organism: Thermotoga maritima (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSDYKDDD DKGSGVTTLS GLSGEQGPSG DMTTEEDSAT HIKFSKRDED GRELAGATME LRDSSGKTIS TWISDGHVKD FYLYPGKYTF VETAAPDGYE VATPIEFTVN EDGQVTVDGE ATEGDAHTGS GGSGGSGMKM EELFKKHKIV AVLRANSVEE AKKKALAVFL ...String:
MGSSDYKDDD DKGSGVTTLS GLSGEQGPSG DMTTEEDSAT HIKFSKRDED GRELAGATME LRDSSGKTIS TWISDGHVKD FYLYPGKYTF VETAAPDGYE VATPIEFTVN EDGQVTVDGE ATEGDAHTGS GGSGGSGMKM EELFKKHKIV AVLRANSVEE AKKKALAVFL GGVHLIEITF TVPDADTVIK ELSFLKEMGA IIGAGTVTSV EQARKAVESG AEFIVSPHLD EEISQFAKEK GVFYMPGVMT PTELVKAMKL GHTILKLFPG EVVGPQFVKA MKGPFPNVKF VPTGGVNLDN VCEWFKAGVL AVGVGSALVK GTPVEVAEKA KAFVEKIRGC TE

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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

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10044 / Average electron dose: 50.1 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: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 1096444
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kp9

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 126295
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5kp9


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsWe used the fit-into map routine in ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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