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- EMDB-43261: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-43261
TitleSARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in complex with SC27 Fab, global refinement
Map data
Sample
  • Complex: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in complex with SC27 Fab, global refinement
    • Complex: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers
    • Complex: SC27 Fab
KeywordsSARS-CoV-2 / coronavirus / S / spike / BA.1 / omicron / RBD / COVID-19 / antibody / SC27 / Fab / virus / viral protein
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsByrne PO / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127521 United States
CitationJournal: Cell Rep Med / Year: 2024
Title: Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.
Authors: William N Voss / Michael A Mallory / Patrick O Byrne / Jeffrey M Marchioni / Sean A Knudson / John M Powers / Sarah R Leist / Bernadeta Dadonaite / Douglas R Townsend / Jessica Kain / Yimin ...Authors: William N Voss / Michael A Mallory / Patrick O Byrne / Jeffrey M Marchioni / Sean A Knudson / John M Powers / Sarah R Leist / Bernadeta Dadonaite / Douglas R Townsend / Jessica Kain / Yimin Huang / Ed Satterwhite / Izabella N Castillo / Melissa Mattocks / Chelsea Paresi / Jennifer E Munt / Trevor Scobey / Allison Seeger / Lakshmanane Premkumar / Jesse D Bloom / George Georgiou / Jason S McLellan / Ralph S Baric / Jason J Lavinder / Gregory C Ippolito /
Abstract: We describe the molecular-level composition of polyclonal immunoglobulin G (IgG) anti-spike antibodies from ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, ...We describe the molecular-level composition of polyclonal immunoglobulin G (IgG) anti-spike antibodies from ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, vaccination, or their combination ("hybrid immunity") at monoclonal resolution. Infection primarily triggers S2/N-terminal domain (NTD)-reactive antibodies, whereas vaccination mainly induces anti-receptor-binding domain (RBD) antibodies. This imprint persists after secondary exposures wherein >60% of ensuing hybrid immunity derives from the original IgG pool. Monoclonal constituents of the original IgG pool can increase breadth, affinity, and prevalence upon secondary exposures, as exemplified by the plasma antibody SC27. Following a breakthrough infection, vaccine-induced SC27 gained neutralization breadth and potency against SARS-CoV-2 variants and zoonotic viruses (half-maximal inhibitory concentration [IC] ∼0.1-1.75 nM) and increased its binding affinity to the protective RBD class 1/4 epitope (dissociation constant [K] < 5 pM). According to polyclonal escape analysis, SC27-like binding patterns are common in SARS-CoV-2 hybrid immunity. Our findings provide a detailed molecular definition of immunological imprinting and show that vaccination can produce class 1/4 (SC27-like) IgG antibodies circulating in the blood.
History
DepositionJan 4, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43261.png

Downloads & links

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Map

FileDownload / File: emd_43261.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 640 pix.
= 601.6 Å		0.94 Å/pix.
x 640 pix.
= 601.6 Å		0.94 Å/pix.
x 640 pix.
= 601.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-1.1508256 - 1.9954618
Average (Standard dev.)-0.00011303895 (±0.01968433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 601.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43261_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43261_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in co...

EntireName: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in complex with SC27 Fab, global refinement
Components
  • Complex: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in complex with SC27 Fab, global refinement
    • Complex: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers
    • Complex: SC27 Fab

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Supramolecule #1: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in co...

SupramoleculeName: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers in complex with SC27 Fab, global refinement
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers

SupramoleculeName: SARS-CoV-2 spike omicron (BA.1) ectodomain dimer-of-trimers
type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: SC27 Fab

SupramoleculeName: SC27 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationName
2.0 mMTris
200.0 mMsodium chloride
0.02 percent (w/v)sodium azide
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Particle selectionNumber selected: 3282579
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 330321
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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