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- EMDB-12530: Subtomogram average of ChAdOx1 nCoV-19/AZD1222 derived SARS-CoV-2... -

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Basic information

Entry
Database: EMDB / ID: EMD-12530
TitleSubtomogram average of ChAdOx1 nCoV-19/AZD1222 derived SARS-CoV-2 spike glycoprotein
Map data
SampleSevere acute respiratory syndrome coronavirus 2:
virus
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 11.6 Å
AuthorsWatanabe Y / Mendonca LM / Allen ER / Howe A / Lee M / Allen JD / Chawla H / Pulido D / Donnellan F / Davies H ...Watanabe Y / Mendonca LM / Allen ER / Howe A / Lee M / Allen JD / Chawla H / Pulido D / Donnellan F / Davies H / Ulaszewska M / Belij-Rammerstorfer S / Morris S / Krebs AS / Dejnirattisai W / Mongkolsapaya J / Supasa P / Screaton GR / Green CM / Lambe T / Zhang P / Gilbert SC / Crispin M
CitationJournal: bioRxiv / Year: 2021
Title: Native-like SARS-CoV-2 spike glycoprotein expressed by ChAdOx1 nCoV-19/AZD1222 vaccine.
Authors: Yasunori Watanabe / Luiza Mendonça / Elizabeth R Allen / Andrew Howe / Mercede Lee / Joel D Allen / Himanshi Chawla / David Pulido / Francesca Donnellan / Hannah Davies / Marta Ulaszewska / ...Authors: Yasunori Watanabe / Luiza Mendonça / Elizabeth R Allen / Andrew Howe / Mercede Lee / Joel D Allen / Himanshi Chawla / David Pulido / Francesca Donnellan / Hannah Davies / Marta Ulaszewska / Sandra Belij-Rammerstorfer / Susan Morris / Anna-Sophia Krebs / Wanwisa Dejnirattisai / Juthathip Mongkolsapaya / Piyada Supasa / Gavin R Screaton / Catherine M Green / Teresa Lambe / Peijun Zhang / Sarah C Gilbert / Max Crispin
Abstract: Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective ...Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirms the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMar 2, 2021-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.71
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.71
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12530.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 177 pix.
= 377.01 Å
2.13 Å/pix.
x 177 pix.
= 377.01 Å
2.13 Å/pix.
x 177 pix.
= 377.01 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density
Contour LevelBy AUTHOR: 4.71 / Movie #1: 4.71
Minimum - Maximum-1.9123931 - 17.348516
Average (Standard dev.)0.10071594 (±0.86205393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions177177177
Spacing177177177
CellA=B=C: 377.01 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z177177177
origin x/y/z0.0000.0000.000
length x/y/z377.010377.010377.010
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS177177177
D min/max/mean-1.91217.3490.101

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Supplemental data

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Sample components

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Entire Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2 / Number of components: 1

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Component #1: virus, Severe acute respiratory syndrome coronavirus 2

VirusName: Severe acute respiratory syndrome coronavirus 2 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C3 (3 fold cyclic) / Number of subtomograms: 11391
3D reconstructionResolution: 11.6 Å / Resolution method: FSC 0.5 CUT-OFF

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