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- EMDB-22301: SARS-CoV-2 Spike D614G variant, minus RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-22301
TitleSARS-CoV-2 Spike D614G variant, minus RBD
Map data
SampleSARS2 Spike D614G:
Spike glycoproteinSpike protein
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / fusion of virus membrane with host endosome membrane / viral entry into host cell / viral envelope / : / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / : ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / : / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang X / Egri SB / Dudkina N / Luban J / Shen K
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI147868 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K22CA241362 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI148784 United States
Citation
Journal: Cell / Year: 2020
Title: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.
Authors: Leonid Yurkovetskiy / Xue Wang / Kristen E Pascal / Christopher Tomkins-Tinch / Thomas P Nyalile / Yetao Wang / Alina Baum / William E Diehl / Ann Dauphin / Claudia Carbone / Kristen ...Authors: Leonid Yurkovetskiy / Xue Wang / Kristen E Pascal / Christopher Tomkins-Tinch / Thomas P Nyalile / Yetao Wang / Alina Baum / William E Diehl / Ann Dauphin / Claudia Carbone / Kristen Veinotte / Shawn B Egri / Stephen F Schaffner / Jacob E Lemieux / James B Munro / Ashique Rafique / Abhi Barve / Pardis C Sabeti / Christos A Kyratsous / Natalya V Dudkina / Kuang Shen / Jeremy Luban /
Abstract: The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral ...The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.
#1: Journal: Biorxiv / Year: 2020
Title: Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Authors: Yurkovetskiy L / Wang X / Pascal KE / Tompkins-Tinch C / Nyalile T / Wang Y / Baum A / Diehl WE / Dauphin A / Carbone C / Veinotte K / Egri SB / Schaffner SF / Lemieux JE / Munro J / Rafique ...Authors: Yurkovetskiy L / Wang X / Pascal KE / Tompkins-Tinch C / Nyalile T / Wang Y / Baum A / Diehl WE / Dauphin A / Carbone C / Veinotte K / Egri SB / Schaffner SF / Lemieux JE / Munro J / Rafique A / Barve A / Sabeti PC / Kyratsous C / Dudkina N / Shen K / Luban J
History
DepositionJul 15, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateNov 11, 2020-
Current statusNov 11, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xs6
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xs6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22301.png

Downloads & links

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Map

FileDownload / File: emd_22301.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 512 pix.
= 266.24 Å		0.52 Å/pix.
x 512 pix.
= 266.24 Å		0.52 Å/pix.
x 512 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.3498438 - 0.9550405
Average (Standard dev.)0.001560422 (±0.01672908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.520.520.52
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.3500.9550.002

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Supplemental data

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Sample components

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Entire SARS2 Spike D614G

EntireName: SARS2 Spike D614G / Number of Components: 2

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Component #1: protein, SARS2 Spike D614G

ProteinName: SARS2 Spike D614G / Recombinant expression: No
MassExperimental: 417 MDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoproteinSpike protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 139.258344 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen 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: 0.6 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C3 (3 fold cyclic) / Number of Projections: 266302
3D reconstructionResolution: 3.7 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6xs6

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