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- EMDB-23097: Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swap... -

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Basic information

Entry
Database: EMDB / ID: EMD-23097
TitleCryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement
Map data
SampleSevere acute respiratory syndrome-related coronavirus spike glycoprotein in complex with domain-swapped antibody 2G12:
spike glycoproteinPeplomer / antibody 2G12 / Spike glycoproteinPeplomer / 2G12 heavy chain / 2G12 light chain / 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
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome-related coronavirus / Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsManne K / Henderson R / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
CitationJournal: bioRxiv / Year: 2020
Title: A glycan cluster on the SARS-CoV-2 spike ectodomain is recognized by Fab-dimerized glycan-reactive antibodies.
Authors: Priyamvada Acharya / Wilton Williams / Rory Henderson / Katarzyna Janowska / Kartik Manne / Robert Parks / Margaret Deyton / Jordan Sprenz / Victoria Stalls / Megan Kopp / Katayoun Mansouri ...Authors: Priyamvada Acharya / Wilton Williams / Rory Henderson / Katarzyna Janowska / Kartik Manne / Robert Parks / Margaret Deyton / Jordan Sprenz / Victoria Stalls / Megan Kopp / Katayoun Mansouri / Robert J Edwards / R Ryan Meyerhoff / Thomas Oguin / Gregory Sempowski / Kevin Saunders / Barton F Haynes
Abstract: The COVID-19 pandemic caused by SARS-CoV-2 has escalated into a global crisis. The spike (S) protein that mediates cell entry and membrane fusion is the current focus of vaccine and therapeutic ...The COVID-19 pandemic caused by SARS-CoV-2 has escalated into a global crisis. The spike (S) protein that mediates cell entry and membrane fusion is the current focus of vaccine and therapeutic antibody development efforts. The S protein, like many other viral fusion proteins such as HIV-1 envelope (Env) and influenza hemagglutinin, is glycosylated with both complex and high mannose glycans. Here we demonstrate binding to the SARS-CoV-2 S protein by a category of Fab-dimerized glycan-reactive (FDG) HIV-1-induced broadly neutralizing antibodies (bnAbs). A 3.1 Å resolution cryo-EM structure of the S protein ectodomain bound to glycan-dependent HIV-1 bnAb 2G12 revealed a quaternary glycan epitope on the spike S2 domain involving multiple protomers. These data reveal a new epitope on the SARS-CoV-2 spike that can be targeted for vaccine design.
Highlights: Fab-dimerized, glycan-reactive (FDG) HIV-1 bnAbs cross-react with SARS-CoV-2 spike.3.1 Å resolution cryo-EM structure reveals quaternary S2 epitope for HIV-1 bnAb 2G12.2G12 targets ...Highlights: Fab-dimerized, glycan-reactive (FDG) HIV-1 bnAbs cross-react with SARS-CoV-2 spike.3.1 Å resolution cryo-EM structure reveals quaternary S2 epitope for HIV-1 bnAb 2G12.2G12 targets glycans, at positions 709, 717 and 801, in the SARS-CoV-2 spike.Our studies suggest a common epitope for FDG antibodies centered around glycan 709.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 11, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.181
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.181
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l09
  • Surface level: 0.181
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23097.png

Downloads & links

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Map

FileDownload / File: emd_23097.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.181 / Movie #1: 0.181
Minimum - Maximum-1.2200918 - 2.3937883
Average (Standard dev.)-0.0022977607 (±0.053766493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 338.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z338.560338.560338.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.2202.394-0.002

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Supplemental data

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Sample components

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Entire Severe acute respiratory syndrome-related coronavirus spike glyco...

EntireName: Severe acute respiratory syndrome-related coronavirus spike glycoprotein in complex with domain-swapped antibody 2G12
Number of components: 7

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Component #1: protein, Severe acute respiratory syndrome-related coronavirus sp...

ProteinName: Severe acute respiratory syndrome-related coronavirus spike glycoprotein in complex with domain-swapped antibody 2G12
Recombinant expression: No

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Component #2: protein, spike glycoprotein

ProteinName: spike glycoproteinPeplomer / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome-related coronavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, antibody 2G12

ProteinName: antibody 2G12 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 124.124477 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, 2G12 heavy chain

ProteinName: 2G12 heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.978051 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, 2G12 light chain

ProteinName: 2G12 light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.24585 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 32 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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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: 66.43 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (93.15 - 93.15 K)
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 222304
3D reconstructionSoftware: cryoSPARC / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Input PDB model: 6VXX

6vxx

Output model

7l09

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