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- EMDB-16404: Subtomogram averaging of a coronavirus spike (ChAdOx1 19E6) in C1... -

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Basic information

Entry
Database: EMDB / ID: EMD-16404
TitleSubtomogram averaging of a coronavirus spike (ChAdOx1 19E6) in C1 symmetry
Map data
Sample
  • Complex: ChAdOx1 coronavirus spike vaccine carrying hexa-proline mutation
KeywordsCoronavirus spike / subtomogram averaging / C1 symmetry / in situ / ChAdOx / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 9.7 Å
AuthorsNi T / Mendonca L / Zhu Y / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: iScience / Year: 2023
Title: ChAdOx1 COVID vaccines express RBD open prefusion SARS-CoV-2 spikes on the cell surface.
Authors: Tao Ni / Luiza Mendonça / Yanan Zhu / Andrew Howe / Julika Radecke / Pranav M Shah / Yuewen Sheng / Anna-Sophia Krebs / Helen M E Duyvesteyn / Elizabeth Allen / Teresa Lambe / Cameron ...Authors: Tao Ni / Luiza Mendonça / Yanan Zhu / Andrew Howe / Julika Radecke / Pranav M Shah / Yuewen Sheng / Anna-Sophia Krebs / Helen M E Duyvesteyn / Elizabeth Allen / Teresa Lambe / Cameron Bisset / Alexandra Spencer / Susan Morris / David I Stuart / Sarah Gilbert / Peijun Zhang /
Abstract: Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proven to be an effective means of decreasing COVID-19 mortality, hospitalization rates, and transmission. One ...Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proven to be an effective means of decreasing COVID-19 mortality, hospitalization rates, and transmission. One of the vaccines deployed worldwide is ChAdOx1 nCoV-19, which uses an adenovirus vector to drive the expression of the original SARS-CoV-2 spike on the surface of transduced cells. Using cryo-electron tomography and subtomogram averaging, we determined the native structures of the vaccine product expressed on cell surfaces . We show that ChAdOx1-vectored vaccines expressing the Beta SARS-CoV-2 variant produce abundant native prefusion spikes predominantly in one-RBD-up conformation. Furthermore, the ChAdOx1-vectored HexaPro-stabilized spike yields higher cell surface expression, enhanced RBD exposure, and reduced shedding of S1 compared to the wild type. We demonstrate structure determination as a powerful means for studying antigen design options in future vaccine development against emerging novel SARS-CoV-2 variants and broadly against other infectious viruses.
History
DepositionDec 27, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16404.png

Downloads & links

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Map

FileDownload / File: emd_16404.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 160 pix.
= 352. Å		2.2 Å/pix.
x 160 pix.
= 352. Å		2.2 Å/pix.
x 160 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.5368428 - 3.413827
Average (Standard dev.)0.011547726 (±0.15071604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16404_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_16404_half_map_2.map
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Sample components

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Entire : ChAdOx1 coronavirus spike vaccine carrying hexa-proline mutation

EntireName: ChAdOx1 coronavirus spike vaccine carrying hexa-proline mutation
Components
  • Complex: ChAdOx1 coronavirus spike vaccine carrying hexa-proline mutation

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Supramolecule #1: ChAdOx1 coronavirus spike vaccine carrying hexa-proline mutation

SupramoleculeName: ChAdOx1 coronavirus spike vaccine carrying hexa-proline mutation
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: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.5 µm / Nominal defocus min: 2.5 µm
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: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: emClarity, RELION) / Number subtomograms used: 28896
ExtractionNumber tomograms: 28896 / Number images used: 28896
Final angle assignmentType: OTHER / Software - Name: emClarity

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