[English] 日本語
Yorodumi
- EMDB-55790: African Horse Sickness Virus serotype 4 VP2 homotrimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55790
TitleAfrican Horse Sickness Virus serotype 4 VP2 homotrimer
Map dataSharp and inverted
Sample
  • Complex: VP2 homotrimer of African horse sickness virus 4.
    • Protein or peptide: Outer capsid protein VP2
  • Ligand: ZINC ION
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 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

-
Structure visualization

Supplemental images

emd_55790.png

Downloads & links

-
Map

FileReleased
AnnotationSharp and inverted
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 330.854 Å		1.29 Å/pix.
x 256 pix.
= 330.854 Å		1.29 Å/pix.
x 256 pix.
= 330.854 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-1.4365562 - 1.8695562
Average (Standard dev.)0.00092415133 (±0.036656905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 330.8544 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55790_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Used for model refinement

Fileemd_55790_additional_1.map
AnnotationUsed for model refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_55790_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half A flipped

Fileemd_55790_half_map_1.map
AnnotationHalf A flipped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half B flipped

Fileemd_55790_half_map_2.map
AnnotationHalf B flipped
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : VP2 homotrimer of African horse sickness virus 4.

EntireName: VP2 homotrimer of African horse sickness virus 4.
Components
  • Complex: VP2 homotrimer of African horse sickness virus 4.
    • Protein or peptide: Outer capsid protein VP2
  • Ligand: ZINC ION

-
Supramolecule #1: VP2 homotrimer of African horse sickness virus 4.

SupramoleculeName: VP2 homotrimer of African horse sickness virus 4. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: The deposited structure is the homotrimer of VP2 protein corresponding to the outer capsid component of AHSV serotype 4.
Source (natural)Organism: African horse sickness virus 4
Molecular weightTheoretical: 124.2 KDa

-
Macromolecule #1: Outer capsid protein VP2

MacromoleculeName: Outer capsid protein VP2 / type: protein_or_peptide / ID: 1
Details: The expressed protein contains a Flag-tag at the N-terminal. The PDB model has two disordered regions (322-328 and 443-448).
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: African horse sickness virus 4
Molecular weightTheoretical: 125.753875 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MDYKDDDDKG SSGMASEFGI LMTNEKFDPS LEKTICDVIV TKKGRVKHKE VDGVCGYEWD ETNHRFGLCE VEHDMSISEF MYNEIRCEG AYPIFPRYII DTLKYEKFID RNDHQIRVDR DDNEMRKILI QPYAGEMYFS PECYPSVFLR REARSQKLDR I RNYIGKRV ...String:
MDYKDDDDKG SSGMASEFGI LMTNEKFDPS LEKTICDVIV TKKGRVKHKE VDGVCGYEWD ETNHRFGLCE VEHDMSISEF MYNEIRCEG AYPIFPRYII DTLKYEKFID RNDHQIRVDR DDNEMRKILI QPYAGEMYFS PECYPSVFLR REARSQKLDR I RNYIGKRV EFYEEESKRK AILDQNKMSK VEQWRDAVNE RIVSIEPKRG ECYDHGTDII YQFIKKLRFG MMYPHYYVLH SD YCIVPNK GGTSIGSWHI RKRTEGDAKA SAMYSGKGPL NDLRVKIERD DLSRETIIQI IEYGKKFNSS AGDKQGNISI EKL VEYCDF LTTFVHAKKK EEGEDDTARQ EIRKAWVKRM PYMDFSKPMK ITRGFNRNML FFAALDSFRK RNGVDVDPNK GKWK EHIKE VTEKLKKAQT ENGGQPCQVS IDGVNVLTNV DYGTVNHWID WVTDIIMVVQ TKRLVKEYAF KKLKSENLLA GMNSL VGVL RCYMYCLALA IYDFYEGTID GFKKGSNASA IIETVAQMFP DFRRELVEKF GIDLRMKEIT RELFVGKSMT SKFMEE GEY GYKFAYGWRR DGFAVMEDYG EILTEKVEDL YKGVLLGRKW EDEVDDPESY FYDDLYTNEP HRVFLSAGKD VDNNITL RS ISQAETTYLS KRFVSYWYRI SQVEVTKARN EVLDMNEKQK PYFEFEYDDF KPCSIGELGI HASTYIYQNL LVGRNRGE E ILDSKELVWM DMSLLNFGAV RSHDRCWISS SVAIEVNLRH ALIVRIFSRF DMMSERETFS TILEKVMEDV KELRFFPTY RHYYLETLQR VFNDERRLEV DDFYMRLYDV QTREQALNTF TDFHRCVESE LLLPTLKLNF LLWIVFEMEN VEVNAAYKRH PLLISTAKG LRVIGVDIFN SQLSISMSGW IPYVERMCAE SKVQTKLTAD ELKLKRWFIS YYTTLKLDRR AEPRMSFKFE G LSTWIGSN CGGVRDYVIQ MLPTRKPKPG ALMVVYARDS RIEWIEAELS QWLQMEGSLG LILVHDSGII NKSVLRARTL KI YNRGSMD TLILISSGVY TFGNKFLLSK LLAKTE

UniProtKB: Outer capsid protein VP2

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.14 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mM(HOCH2)3CNH3ClTris-HCl
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsPlease, see publication.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 18125 / Average electron dose: 52.7 e/Å2
Details: From the total: 4007 at +30 degrees tilt and 14118 at -30 degrees tilt
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

+
Image processing

Particle selectionNumber selected: 4772633
CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Modelangelo and Alphafold
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Details: Please, see the publication. / Number images used: 381372
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico modelAlphafold2
source_name: Other, initial_model_type: integrative modelModelAngelo
RefinementSpace: REAL / Protocol: OTHER
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more