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- EMDB-60602: SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced... -

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Basic information

Entry
Database: EMDB / ID: EMD-60602
TitleSARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced by Ad5-nCoV vaccine
Map data
Sample
  • Complex: SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced by Ad5-nCoV vaccine
KeywordsSARS-CoV-2 / spike / vaccine / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsDong D / Song Y / Li S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2025
Title: Molecular basis of Ad5-nCoV vaccine-induced immunogenicity.
Authors: Dongyang Dong / Yutong Song / Shipo Wu / Busen Wang / Cheng Peng / Weiping Zhang / Weizheng Kong / Zheyuan Zhang / Jingwen Song / Li-Hua Hou / Sai Li /
Abstract: Ad5-nCoV (Convidecia) is listed for emergency use against COVID-19 by the World Health Organization (WHO) and has been globally administered to millions of people. It utilizes human adenovirus 5 (Ad5) ...Ad5-nCoV (Convidecia) is listed for emergency use against COVID-19 by the World Health Organization (WHO) and has been globally administered to millions of people. It utilizes human adenovirus 5 (Ad5) replication-incompetent vector to deliver the spike (S) protein gene from various SARS-CoV-2 strains. Despite promising clinical data, the molecular mechanism underlying its high immunogenicity and adverse reactions remain incompletely understood. Here, we primarily applied cryo-electron tomography (cryo-ET), fluorescence microscopy and mass spectrometry to analyze the Ad5-nCoV_Wu and Ad5-nCoV_O vaccine-induced S antigens. These antigens encode the unmodified SARS-CoV-2 Wuhan-Hu-1 S gene and the stabilized Omicron S gene, respectively. Our findings highlight the structural integrity, antigenicity, and dense distribution on cell membrane of the vaccine-induced S proteins. Ad5-nCoV_O induced S proteins exhibit improved stability and reduced syncytia formation among inoculated cells. Our work demonstrates that Ad5-nCoV is a prominent platform for antigen induction and cryo-ET can be a useful technique for vaccine characterization and development.
History
DepositionJun 21, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60602.png

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Map

FileDownload / File: emd_60602.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
3.28 Å/pix.
x 144 pix.
= 472.32 Å		3.28 Å/pix.
x 144 pix.
= 472.32 Å		3.28 Å/pix.
x 144 pix.
= 472.32 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.28 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 4.2
Minimum - Maximum-6.5986686 - 18.856241000000001
Average (Standard dev.)-0.0068509355 (±0.8559085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 472.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60602_msk_1.map
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Half map: #1

Fileemd_60602_half_map_1.map
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Half map: #2

Fileemd_60602_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced...

EntireName: SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced by Ad5-nCoV vaccine
Components
  • Complex: SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced by Ad5-nCoV vaccine

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Supramolecule #1: SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced...

SupramoleculeName: SARS-CoV-2 spike (Omicron) in the One-RBD-up conformation induced by Ad5-nCoV vaccine
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 53000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 11424
ExtractionNumber tomograms: 40 / Number images used: 18110
CTF correctionSoftware - Name: NOVACTF / Type: PHASE FLIPPING ONLY
Final 3D classificationSoftware - Name: Dynamo
Final angle assignmentType: OTHER / Software - Name: Dynamo
FSC plot (resolution estimation)

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