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- PDB-9tcc: African Horse Sickness Virus serotype 4 VP2 homotrimer -

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Basic information

Entry
Database: PDB / ID: 9tcc
TitleAfrican Horse Sickness Virus serotype 4 VP2 homotrimer
ComponentsOuter capsid protein VP2
KeywordsVIRAL PROTEIN / serotype determinant / protective inmmunity
Function / homologyOuter capsid protein VP2, Orbivirus / Orbivirus outer capsid protein VP2 / viral inner capsid / structural molecule activity / Outer capsid protein VP2
Function and homology information
Biological speciesAfrican horse sickness virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsMartinez-Castillo, A. / Aebischer, A. / Fu, L. / Breard, E. / Zientara, S. / Kortekaas, J. / Beer, M. / Abrescia, N.G.A.
Funding supportEuropean Union, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer capsid protein VP2
B: Outer capsid protein VP2
C: Outer capsid protein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,4586
Polymers377,2623
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Outer capsid protein VP2


Mass: 125753.875 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The expressed protein contains a Flag-tag at the N-terminal. The PDB model has two disordered regions (322-328 and 443-448).
Source: (gene. exp.) African horse sickness virus 4 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: A0A0B5GT51
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: VP2 homotrimer of African horse sickness virus 4. / Type: COMPLEX
Details: The deposited structure is the homotrimer of VP2 protein corresponding to the outer capsid component of AHSV serotype 4.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.1242 MDa / Experimental value: NO
Source (natural)Organism: African horse sickness virus 4
Source (recombinant)Organism: BSR
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl(HOCH2)3CNH3Cl1
2150 mMSodium ChlorideNaCl1
SpecimenConc.: 0.14 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Please, see publication.
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18125
Details: From the total: 4007 at +30 degrees tilt and 14118 at -30 degrees tilt

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4cryoSPARC4CTF correction
7Coot0.8model fitting
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11cryoSPARC4classification
12cryoSPARC43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4772633
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 381372 / Details: Please, see the publication. / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
ID 3D fitting-IDDetails (eV)Source nameType
11Alphafold2AlphaFoldin silico model
21ModelAngeloOtherintegrative model
RefinementHighest resolution: 3.11 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226418
ELECTRON MICROSCOPYf_angle_d0.36835568
ELECTRON MICROSCOPYf_dihedral_angle_d9.44610008
ELECTRON MICROSCOPYf_chiral_restr0.0383786
ELECTRON MICROSCOPYf_plane_restr0.0034536

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