+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15182 | ||||||||||||
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Title | Electron cryotomography of SARS-CoV-2 virions | ||||||||||||
Map data | Cryo Tomogram of SARS_Cov2 Wuhan viral particles | ||||||||||||
Sample |
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Keywords | SARS-CoV-2 / lipid-enveloped virus / spike glycoprotein / receptor binding / VIRUS | ||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Calder LJ / Calcraft T / Hussain S / Harvey R / Rosenthal PB | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Commun Biol / Year: 2022 Title: Electron cryotomography of SARS-CoV-2 virions reveals cylinder-shaped particles with a double layer RNP assembly. Authors: Lesley J Calder / Thomas Calcraft / Saira Hussain / Ruth Harvey / Peter B Rosenthal / Abstract: SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov- ...SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov-2 virions and three variants revealing particles of regular cylindrical morphology. The ribonucleoprotein particles packaging the genome in the virion interior form a dense, double layer assembly with a cylindrical shape related to the overall particle morphology. This organisation suggests structural interactions important to virus assembly. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15182.map.gz | 388.2 MB | EMDB map data format | |
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Header (meta data) | emd-15182-v30.xml emd-15182.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_15182.png | 196.9 KB | ||
Filedesc metadata | emd-15182.cif.gz | 4.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15182 | HTTPS FTP |
-Validation report
Summary document | emd_15182_validation.pdf.gz | 504.6 KB | Display | EMDB validaton report |
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Full document | emd_15182_full_validation.pdf.gz | 504.1 KB | Display | |
Data in XML | emd_15182_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_15182_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15182 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15182 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15182.map.gz / Format: CCP4 / Size: 426.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo Tomogram of SARS_Cov2 Wuhan viral particles | ||||||||||||||||||||
Voxel size | X=Y=Z: 8.8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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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 / Details: Virus grown in Vero V1 cells and purified / NCBI-ID: 2697049 Sci species name: Severe acute respiratory syndrome coronavirus 2 Sci species strain: Wuhan / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: BBI Solutions / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV |
Details | Tilt series collected using dose symmetric scheme. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-4 / Number real images: 41 / Average exposure time: 1.7 sec. / Average electron dose: 2.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000 |
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 | Algorithm: BACK PROJECTION Software:
Number images used: 41 |
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