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Yorodumi- EMDB-12991: SARS-CoV-2 spike subtomogram average from extracelullar viruses -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12991 | |||||||||
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Title | SARS-CoV-2 spike subtomogram average from extracelullar viruses | |||||||||
Map data | SARS-CoV-2 spike from extracellular viruses | |||||||||
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 / 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 | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 10.6 Å | |||||||||
Authors | Mendonca L / Zhang P | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress. Authors: Luiza Mendonça / Andrew Howe / James B Gilchrist / Yuewen Sheng / Dapeng Sun / Michael L Knight / Laura C Zanetti-Domingues / Benji Bateman / Anna-Sophia Krebs / Long Chen / Julika Radecke ...Authors: Luiza Mendonça / Andrew Howe / James B Gilchrist / Yuewen Sheng / Dapeng Sun / Michael L Knight / Laura C Zanetti-Domingues / Benji Bateman / Anna-Sophia Krebs / Long Chen / Julika Radecke / Vivian D Li / Tao Ni / Ilias Kounatidis / Mohamed A Koronfel / Marta Szynkiewicz / Maria Harkiolaki / Marisa L Martin-Fernandez / William James / Peijun Zhang / Abstract: Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how ...Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events - e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules. | |||||||||
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_12991.map.gz | 3.3 MB | EMDB map data format | |
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Header (meta data) | emd-12991-v30.xml emd-12991.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_12991.png | 51.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12991 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12991 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10753 (Title: Tilt-series taken from SARS-CoV-2 infected Vero cells. Data size: 52.7 Data #1: Tilt-series taken on the periphery of SARS-CoV-2 infected Vero cells [tilt series] Data #2: Tilt-series taken on cryolamella of SARS-CoV-2 infected Vero cells [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12991.map.gz / Format: CCP4 / Size: 41.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 spike from extracellular viruses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 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: 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: 7.2 / Details: 4% parafolmaldehyde in phosphate buffered saline |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 10 / Number images used: 2179 |
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CTF correction | Software - Name: emClarity (ver. 1.5.3.03) |
Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 2179 |