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- EMDB-21965: Negative stain EM map of SARS CoV-2 spike protein (trimer) -

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Basic information

Entry
Database: EMDB / ID: EMD-21965
TitleNegative stain EM map of SARS CoV-2 spike protein (trimer)
Map dataSRAS Cov2 spike protein (trimer)
Sample
  • Complex: SARS CoV-2 spike protein (trimer)
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsBinshtein E
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)HR0011-18-2-0001 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00074 United States
CitationJournal: Nature / Year: 2020
Title: Potently neutralizing and protective human antibodies against SARS-CoV-2.
Authors: Seth J Zost / Pavlo Gilchuk / James Brett Case / Elad Binshtein / Rita E Chen / Joseph P Nkolola / Alexandra Schäfer / Joseph X Reidy / Andrew Trivette / Rachel S Nargi / Rachel E Sutton / ...Authors: Seth J Zost / Pavlo Gilchuk / James Brett Case / Elad Binshtein / Rita E Chen / Joseph P Nkolola / Alexandra Schäfer / Joseph X Reidy / Andrew Trivette / Rachel S Nargi / Rachel E Sutton / Naveenchandra Suryadevara / David R Martinez / Lauren E Williamson / Elaine C Chen / Taylor Jones / Samuel Day / Luke Myers / Ahmed O Hassan / Natasha M Kafai / Emma S Winkler / Julie M Fox / Swathi Shrihari / Benjamin K Mueller / Jens Meiler / Abishek Chandrashekar / Noe B Mercado / James J Steinhardt / Kuishu Ren / Yueh-Ming Loo / Nicole L Kallewaard / Broc T McCune / Shamus P Keeler / Michael J Holtzman / Dan H Barouch / Lisa E Gralinski / Ralph S Baric / Larissa B Thackray / Michael S Diamond / Robert H Carnahan / James E Crowe /
Abstract: The ongoing pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major threat to global health and the medical ...The ongoing pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major threat to global health and the medical countermeasures available so far are limited. Moreover, we currently lack a thorough understanding of the mechanisms of humoral immunity to SARS-CoV-2. Here we analyse a large panel of human monoclonal antibodies that target the spike (S) glycoprotein, and identify several that exhibit potent neutralizing activity and fully block the receptor-binding domain of the S protein (S) from interacting with human angiotensin-converting enzyme 2 (ACE2). Using competition-binding, structural and functional studies, we show that the monoclonal antibodies can be clustered into classes that recognize distinct epitopes on the S, as well as distinct conformational states of the S trimer. Two potently neutralizing monoclonal antibodies, COV2-2196 and COV2-2130, which recognize non-overlapping sites, bound simultaneously to the S protein and neutralized wild-type SARS-CoV-2 virus in a synergistic manner. In two mouse models of SARS-CoV-2 infection, passive transfer of COV2-2196, COV2-2130 or a combination of both of these antibodies protected mice from weight loss and reduced the viral burden and levels of inflammation in the lungs. In addition, passive transfer of either of two of the most potent ACE2-blocking monoclonal antibodies (COV2-2196 or COV2-2381) as monotherapy protected rhesus macaques from SARS-CoV-2 infection. These results identify protective epitopes on the S and provide a structure-based framework for rational vaccine design and the selection of robust immunotherapeutic agents.
History
DepositionMay 12, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateSep 2, 2020-
Current statusSep 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21965.png

Downloads & links

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Map

FileDownload / File: emd_21965.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSRAS Cov2 spike protein (trimer)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-5.9280267 - 16.339407
Average (Standard dev.)-0.17492658 (±0.71872044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.364.364.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
start NX/NY/NZ13112264
NX/NY/NZ123151209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-5.92816.339-0.175

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Supplemental data

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Sample components

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Entire : SARS CoV-2 spike protein (trimer)

EntireName: SARS CoV-2 spike protein (trimer)
Components
  • Complex: SARS CoV-2 spike protein (trimer)

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Supramolecule #1: SARS CoV-2 spike protein (trimer)

SupramoleculeName: SARS CoV-2 spike protein (trimer) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 8 / Component:
ConcentrationName
2.0 mMTris
200.0 mMNaCl
StainingType: NEGATIVE / Material: UF
GridMaterial: COPPER / Mesh: 400

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 122 / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3585
CTF correctionSoftware - Name: cryoSPARC (ver. 2.14.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Number images used: 2188
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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