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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 dataChAdOx1 nCoV-19 derived spike glycoprotein
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
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.
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

emd_12530.png

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)
AnnotationChAdOx1 nCoV-19 derived spike glycoprotein
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
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 57 / Number images used: 11391
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.6 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 11391

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