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- EMDB-23155: Negative stain EM map of SARS-CoV-2 spike protein (trimer) with F... -

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Basic information

Entry
Database: EMDB / ID: EMD-23155
TitleNegative stain EM map of SARS-CoV-2 spike protein (trimer) with Fab COV2-2676 (NTD)
Map data
Sample
  • Complex: SARS-COV-2 spike protein (trimer) with Fab COV2-2676
    • Complex: SARS-COV-2 spike protein (trimer)
    • Complex: Fab COV2-2676
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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsBinshtein E / Crowe JE
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
Citation
Journal: bioRxiv / Year: 2021
Title: Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein.
Authors: Naveenchandra Suryadevara / Swathi Shrihari / Pavlo Gilchuk / Laura A VanBlargan / Elad Binshtein / Seth J Zost / Rachel S Nargi / Rachel E Sutton / Emma S Winkler / Elaine C Chen / Mallorie ...Authors: Naveenchandra Suryadevara / Swathi Shrihari / Pavlo Gilchuk / Laura A VanBlargan / Elad Binshtein / Seth J Zost / Rachel S Nargi / Rachel E Sutton / Emma S Winkler / Elaine C Chen / Mallorie E Fouch / Edgar Davidson / Benjamin J Doranz / Robert H Carnahan / Larissa B Thackray / Michael S Diamond / James E Crowe
Abstract: Most human monoclonal antibodies (mAbs) neutralizing SARS-CoV-2 recognize the spike (S) protein receptor-binding domain and block virus interactions with the cellular receptor angiotensin-converting ...Most human monoclonal antibodies (mAbs) neutralizing SARS-CoV-2 recognize the spike (S) protein receptor-binding domain and block virus interactions with the cellular receptor angiotensin-converting enzyme 2. We describe a panel of human mAbs binding to diverse epitopes on the N-terminal domain (NTD) of S protein from SARS-CoV-2 convalescent donors and found a minority of these possessed neutralizing activity. Two mAbs (COV2-2676 and COV2-2489) inhibited infection of authentic SARS-CoV-2 and recombinant VSV/SARS-CoV-2 viruses. We mapped their binding epitopes by alanine-scanning mutagenesis and selection of functional SARS-CoV-2 S neutralization escape variants. Mechanistic studies showed that these antibodies neutralize in part by inhibiting a post-attachment step in the infection cycle. COV2-2676 and COV2-2489 offered protection either as prophylaxis or therapy, and Fc effector functions were required for optimal protection. Thus, natural infection induces a subset of potent NTD-specific mAbs that leverage neutralizing and Fc-mediated activities to protect against SARS-CoV-2 infection using multiple functional attributes.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2021
Title: Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein.
Authors: Suryadevara N / Shrihari S / Gilchuk P / VanBlargan LA / Binshtein E / Zost SJ / Nargi RS / Sutton RE / Winkler ES / Chen EC / Fouch ME / Davidson E / Doranz BJ / Chen RE / Shi PY / Carnahan ...Authors: Suryadevara N / Shrihari S / Gilchuk P / VanBlargan LA / Binshtein E / Zost SJ / Nargi RS / Sutton RE / Winkler ES / Chen EC / Fouch ME / Davidson E / Doranz BJ / Chen RE / Shi PY / Carnahan RH / Thackray LB / Diamond MS / Crowe Jr JE
History
DepositionDec 17, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23155.png

Downloads & links

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Map

FileDownload / File: emd_23155.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.)
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: 2.0 / Movie #1: 2
Minimum - Maximum-6.772925 - 22.909615
Average (Standard dev.)-0.22098507 (±1.1692953)
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/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-6.77322.910-0.221

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Supplemental data

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Sample components

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Entire : SARS-COV-2 spike protein (trimer) with Fab COV2-2676

EntireName: SARS-COV-2 spike protein (trimer) with Fab COV2-2676
Components
  • Complex: SARS-COV-2 spike protein (trimer) with Fab COV2-2676
    • Complex: SARS-COV-2 spike protein (trimer)
    • Complex: Fab COV2-2676

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Supramolecule #1: SARS-COV-2 spike protein (trimer) with Fab COV2-2676

SupramoleculeName: SARS-COV-2 spike protein (trimer) with Fab COV2-2676 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SARS-COV-2 spike protein (trimer)

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

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Supramolecule #3: Fab COV2-2676

SupramoleculeName: Fab COV2-2676 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
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:
ConcentrationNameFormula
20.0 mMTris
200.0 mMsodium chlorideNaCl
StainingType: NEGATIVE / Material: UF
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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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: 376 / Average electron dose: 30.0 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: 1.9000000000000001 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: 44443
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 4859
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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