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- EMDB-54413: Composite density map of Chikungunya virus-like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-54413
TitleComposite density map of Chikungunya virus-like particle
Map data
Sample
  • Complex: Chikungunya Virus-like particle
Keywordscryo-EM structure / Chikungunya virus / VLP / Virus / Localized reconstruction
Biological speciesChikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSong X / Kim YC / Huiskonen JT
Funding support Finland, 1 items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: Npj Viruses / Year: 2026
Title: Structural and immunogenic characterisation of ChAdOx1 Chik-derived Chikungunya VLPs supports a mechanistic rationale for vaccine-induced protection.
Authors: Young Chan Kim / Xiyong Song / Yasunori Watanabe / Raquel de Oliveira Souza / Robert Stass / Sthefany Pagliari / Max Crispin / Beate Mareike Kümmerer / Carla Claser / Thomas A Bowden / Juha ...Authors: Young Chan Kim / Xiyong Song / Yasunori Watanabe / Raquel de Oliveira Souza / Robert Stass / Sthefany Pagliari / Max Crispin / Beate Mareike Kümmerer / Carla Claser / Thomas A Bowden / Juha T Huiskonen / Arturo Reyes-Sandoval /
Abstract: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes severe chronic arthritis in humans and constitutes an expanding global threat. We previously reported that a single unadjuvanted ...Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes severe chronic arthritis in humans and constitutes an expanding global threat. We previously reported that a single unadjuvanted dose of ChAdOx1 Chik vaccine was safe and elicited cross-protective functional antibodies against four distinctive CHIKV lineages in a Phase 1 trial. Here, we show that the CHIKV structural polyprotein encoded by ChAdOx1 Chik can assemble into CHIKV virus-like particles (VLPs) in mammalian cells. Cryo-EM derived reconstruction confirms that these CHIKV VLPs closely resemble the structure of the native virion and LC-MS demonstrates authentic E1/E2 glycosylation. In C57BL/6 mice, unadjuvanted CHIKV VLPs conferred significant protection against viremia and CHIKV-induced foot swelling. A head-to-head comparison of three adjuvant-free platforms encoding structural antigens derived from ChAdOx1 Chik showed that viral-vectors and VLPs induced similar CHIKV-neutralising antibody titres, both surpassing immunisation with soluble E2. Together, these structural and immunogenicity data support a mechanistic rationale that VLP assembly mediated by the clinically relevant ChAdOx1 Chik vaccine contributes to its vaccine-induced protection demonstrated in pre-clinical and clinical studies.
History
DepositionJul 16, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 800 pix.
= 867.2 Å
1.08 Å/pix.
x 800 pix.
= 867.2 Å
1.08 Å/pix.
x 800 pix.
= 867.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.04757386 - 0.0958367
Average (Standard dev.)0.00010254231 (±0.0047755865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 867.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Chikungunya Virus-like particle

EntireName: Chikungunya Virus-like particle
Components
  • Complex: Chikungunya Virus-like particle

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Supramolecule #1: Chikungunya Virus-like particle

SupramoleculeName: Chikungunya Virus-like particle / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chikungunya virus

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: CTFFIND, RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Scipion / Number images used: 658141
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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