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- EMDB-11496: Subtomogram averaging of SARS-CoV-2 spike protein from unconcentr... -

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Basic information

Entry
Database: EMDB / ID: EMD-11496
TitleSubtomogram averaging of SARS-CoV-2 spike protein from unconcentrated virions: Prefusion Class (2 open RBDs)
Map data
SampleSevere acute respiratory syndrome coronavirus 2:
virus / SARS-CoV-2 Spike proteins on virions
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
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 9.9 Å
AuthorsKe Z / Oton J / Zivanov J / Lu JM / Peukes J / Cortese M / Zila V / Scheres SHW / Briggs JAG
Funding supportEuropean Union, United Kingdom, Japan, Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432European Union
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1013 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
Japan Society for the Promotion of Science (JSPS) Japan
German Research Foundation (DFG)240245660-SFB 1129 Germany
CitationJournal: 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 ReportSummary, Full report, XML, About validation report
History
DepositionJul 28, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11496.png

Downloads & links

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Map

FileDownload / File: emd_11496.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.06 Å/pix.
x 128 pix.
= 392.192 Å		3.06 Å/pix.
x 128 pix.
= 392.192 Å		3.06 Å/pix.
x 128 pix.
= 392.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-3.9059904 - 15.108139
Average (Standard dev.)-0.025958644 (±0.8509294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 392.192 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.0643.0643.064
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z392.192392.192392.192
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-3.90615.108-0.026

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Supplemental data

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Half map: prefusion 2 open RBDs, half1

Fileemd_11496_half_map_1.map
Annotationprefusion 2 open RBDs, half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: prefusion 2 open RBDs, half2

Fileemd_11496_half_map_2.map
Annotationprefusion 2 open RBDs, half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Details: Unconcentrated supernatant of SARS-CoV-2 virions produced from infected VeroE6 cells.
Number of components: 2

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Component #1: virus, Severe acute respiratory syndrome coronavirus 2

VirusName: Severe acute respiratory syndrome coronavirus 2 / Class: VIRION
Details: Unconcentrated supernatant of SARS-CoV-2 virions produced from infected VeroE6 cells.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Severe acute respiratory syndrome coronavirus 2

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Component #2: protein, SARS-CoV-2 Spike proteins on virions

ProteinName: SARS-CoV-2 Spike proteins on virions / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2 / Strain: Germany/BavPat1/2020

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 6000.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 µm

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 525
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: novaCTF Relion dedicated python script / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Modified version of RELION for subtomogram averaging
Euler angles: Modified version of RELION for subtomogram averaging

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