|Entry||Database: EMDB / ID: EMD-11497|
|Title||Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs|
|Sample||Severe acute respiratory syndrome coronavirus 2:|
virus / Spike glycoproteinPeplomer / ligand
|Function / homology|
Function and homology information
suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike glycoprotein S2, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal
|Biological species||Severe acute respiratory syndrome coronavirus 2 / 2019-nCoV (virus)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.5 Å|
|Authors||Ke Z / Qu K / Nakane T / Xiong X / Cortese M / Zila V / Scheres SHW / Briggs JAG|
|Funding support||European Union, United Kingdom, Japan, Germany, 5 items |
|Citation||Journal: Nature / Year: 2020|
Title: Structures and distributions of SARS-CoV-2 spike proteins on intact virions.
Authors: Zunlong Ke / Joaquin Oton / Kun Qu / Mirko Cortese / Vojtech Zila / Lesley McKeane / Takanori Nakane / Jasenko Zivanov / Christopher J Neufeldt / Berati Cerikan / John M Lu / Julia Peukes / ...Authors: Zunlong Ke / Joaquin Oton / Kun Qu / Mirko Cortese / Vojtech Zila / Lesley McKeane / Takanori Nakane / Jasenko Zivanov / Christopher J Neufeldt / Berati Cerikan / John M Lu / Julia Peukes / Xiaoli Xiong / Hans-Georg Kräusslich / Sjors H W Scheres / Ralf Bartenschlager / John A G Briggs /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude. Heavily glycosylated S trimers bind to the ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude. Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor and mediate entry of virions into target cells. S exhibits extensive conformational flexibility: it modulates exposure of its receptor-binding site and subsequently undergoes complete structural rearrangement to drive fusion of viral and cellular membranes. The structures and conformations of soluble, overexpressed, purified S proteins have been studied in detail using cryo-electron microscopy, but the structure and distribution of S on the virion surface remain unknown. Here we applied cryo-electron microscopy and tomography to image intact SARS-CoV-2 virions and determine the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. These results reveal the conformations of S on the virion, and provide a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_11497.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.061 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Half map: #2
|Projections & Slices|
-Half map: #1
-Entire Severe acute respiratory syndrome coronavirus 2
|Entire||Name: Severe acute respiratory syndrome coronavirus 2|
Details: sucrose-cushion purified SARS-CoV-2 virions produced from infected VeroE6 cells.
Number of components: 3
-Component #1: virus, Severe acute respiratory syndrome coronavirus 2
|Virus||Name: Severe acute respiratory syndrome coronavirus 2 / Class: VIRION|
Details: sucrose-cushion purified SARS-CoV-2 virions produced from infected VeroE6 cells.
Empty: No / Enveloped: Yes / Isolate: STRAIN
|Species||Species: Severe acute respiratory syndrome coronavirus 2 / Strain: Germany/BavPat1/2020|
-Component #2: protein, Spike glycoprotein
|Protein||Name: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 141.239391 kDa|
|Source||Species: 2019-nCoV (virus)|
-Component #3: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose
|Ligand||Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 33 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm / Energy filter: GIF Bioquantum|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image acquisition||Number of digital images: 7982 / Sampling size: 5 µm|
|Processing||Method: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 29183|
|3D reconstruction||Software: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-Aug 12, 2020. New: Covid-19 info
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Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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