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Yorodumi- EMDB-12530: Subtomogram average of ChAdOx1 nCoV-19/AZD1222 derived SARS-CoV-2... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12530 | |||||||||
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Title | Subtomogram average of ChAdOx1 nCoV-19/AZD1222 derived SARS-CoV-2 spike glycoprotein | |||||||||
Map data | ChAdOx1 nCoV-19 derived spike glycoprotein | |||||||||
Sample |
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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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 11.6 Å | |||||||||
Authors | Watanabe 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 | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12530.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-12530-v30.xml emd-12530.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_12530.png | 52.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12530 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12530 | HTTPS FTP |
-Validation report
Summary document | emd_12530_validation.pdf.gz | 183.6 KB | Display | EMDB validaton report |
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Full document | emd_12530_full_validation.pdf.gz | 182.7 KB | Display | |
Data in XML | emd_12530_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12530 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12530 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12530.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ChAdOx1 nCoV-19 derived spike glycoprotein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Severe acute respiratory syndrome coronavirus 2
Entire | Name: Severe acute respiratory syndrome coronavirus 2 |
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Components |
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-Supramolecule #1: Severe acute respiratory syndrome coronavirus 2
Supramolecule | Name: 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 |
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Host system | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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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Extraction | Number tomograms: 57 / Number images used: 11391 |
Final angle assignment | Type: OTHER |