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- EMDB-28850: SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-28850
TitleSARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab
Map dataGamma 6P Mut7 COVA309-3
Sample
  • Complex: SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab
Keywordscoronavirus / SARS-CoV-2 / COVID / structural protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTorres JL / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: iScience / Year: 2023
Title: Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual.
Authors: Denise Guerra / Tim Beaumont / Laura Radić / Gius Kerster / Karlijn van der Straten / Meng Yuan / Jonathan L Torres / Wen-Hsin Lee / Hejun Liu / Meliawati Poniman / Ilja Bontjer / Judith A ...Authors: Denise Guerra / Tim Beaumont / Laura Radić / Gius Kerster / Karlijn van der Straten / Meng Yuan / Jonathan L Torres / Wen-Hsin Lee / Hejun Liu / Meliawati Poniman / Ilja Bontjer / Judith A Burger / Mathieu Claireaux / Tom G Caniels / Jonne L Snitselaar / Tom P L Bijl / Sabine Kruijer / Gabriel Ozorowski / David Gideonse / Kwinten Sliepen / Andrew B Ward / Dirk Eggink / Godelieve J de Bree / Ian A Wilson / Rogier W Sanders / Marit J van Gils /
Abstract: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and ...The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants. A stabilized spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants, with COVA309-35 being the most potent against the autologous virus, as well as Omicron BA.1 and BA.2, and COVA309-22 having binding and neutralization activity against Omicron BA.4/5, BQ.1.1, and XBB.1. When combining the COVA309 mAbs as cocktails or bispecific antibodies, the breadth and potency were improved. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.
History
DepositionNov 10, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28850.png

Downloads & links

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Map

FileDownload / File: emd_28850.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGamma 6P Mut7 COVA309-3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0259
Minimum - Maximum-0.04064719 - 0.10572489
Average (Standard dev.)-0.000034182627 (±0.0043687574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Gamma 6P Mut7 COVA309-3

Fileemd_28850_half_map_1.map
AnnotationGamma 6P Mut7 COVA309-3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gamma 6P Mut7 COVA309-3

Fileemd_28850_half_map_2.map
AnnotationGamma 6P Mut7 COVA309-3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab

EntireName: SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab
Components
  • Complex: SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab

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Supramolecule #1: SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab

SupramoleculeName: SARS-CoV-2 Gamma 6P Mut7 S + COVA309-3 Fab / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: 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

BufferpH: 7.4
StainingType: NEGATIVE / Material: 2% Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 19302
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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