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Yorodumi- EMDB-11627: Subtomogram average of beta-propiolactone-treated SARS-CoV-2 post... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11627 | |||||||||
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Title | Subtomogram average of beta-propiolactone-treated SARS-CoV-2 post-fusion spike | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 10.7 Å | |||||||||
Authors | Mendonca LM / Liu C / Yang Y / Gao Y / Shen C / Liu J / Ni T / Ju B / Tang X / Wei J ...Mendonca LM / Liu C / Yang Y / Gao Y / Shen C / Liu J / Ni T / Ju B / Tang X / Wei J / Ma X / Zhu Y / Liu W / Xu S / Liu Y / Yuan J / Wu J / Liu Z / Zhang Z / Liu L / Wang P / Zhang P | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2020 Title: The Architecture of Inactivated SARS-CoV-2 with Postfusion Spikes Revealed by Cryo-EM and Cryo-ET. Authors: Chuang Liu / Luiza Mendonça / Yang Yang / Yuanzhu Gao / Chenguang Shen / Jiwei Liu / Tao Ni / Bin Ju / Congcong Liu / Xian Tang / Jinli Wei / Xiaomin Ma / Yanan Zhu / Weilong Liu / Shuman ...Authors: Chuang Liu / Luiza Mendonça / Yang Yang / Yuanzhu Gao / Chenguang Shen / Jiwei Liu / Tao Ni / Bin Ju / Congcong Liu / Xian Tang / Jinli Wei / Xiaomin Ma / Yanan Zhu / Weilong Liu / Shuman Xu / Yingxia Liu / Jing Yuan / Jing Wu / Zheng Liu / Zheng Zhang / Lei Liu / Peiyi Wang / Peijun Zhang / Abstract: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) resulted from the outbreak of SARS-CoV-2 in December 2019. Currently, multiple efforts are being made to rapidly develop vaccines ...The ongoing global pandemic of coronavirus disease 2019 (COVID-19) resulted from the outbreak of SARS-CoV-2 in December 2019. Currently, multiple efforts are being made to rapidly develop vaccines and treatments to fight COVID-19. Current vaccine candidates use inactivated SARS-CoV-2 viruses; therefore, it is important to understand the architecture of inactivated SARS-CoV-2. We have genetically and structurally characterized β-propiolactone-inactivated viruses from a propagated and purified clinical strain of SARS-CoV-2. We observed that the virus particles are roughly spherical or moderately pleiomorphic. Although a small fraction of prefusion spikes are found, most spikes appear nail shaped, thus resembling a postfusion state, where the S1 protein of the spike has disassociated from S2. Cryoelectron tomography and subtomogram averaging of these spikes yielded a density map that closely matches the overall structure of the SARS-CoV postfusion spike and its corresponding glycosylation site. Our findings have major implications for SARS-CoV-2 vaccine design, especially those using inactivated viruses. | |||||||||
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_11627.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-11627-v30.xml emd-11627.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
Images | emd_11627.png | 31.1 KB | ||
Others | emd_11627_half_map_1.map.gz emd_11627_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11627 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11627 | HTTPS FTP |
-Validation report
Summary document | emd_11627_validation.pdf.gz | 424.4 KB | Display | EMDB validaton report |
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Full document | emd_11627_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | emd_11627_validation.xml.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11627 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11627 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11627.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_11627_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11627_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Yes / Virus empty: No |
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-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 | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-10 / Average electron dose: 2.55 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: 10.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 956 |
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Extraction | Number tomograms: 242 / Number images used: 956 Method: Manual picking combined with surface model orientation |
Final angle assignment | Type: OTHER / Software - Name: Dynamo Details: Initial angles based on oriented surface model (normal to viral membrane), and refined based on iterative subtomogram alignment. |