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- EMDB-25011: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs compl... -

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Entry
Database: EMDB / ID: EMD-25011
TitleSpike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Map data3D refined map of HKU1 spike with donor 1988 polyclonal Fabs (C1 symmetry)
Sample
  • Complex: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Biological speciesHuman coronavirus OC43
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsWard AB / Bangaru S / Sewall LM / Jackson AM
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structural mapping of antibody landscapes to human betacoronavirus spike proteins.
Authors: Sandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents ...Authors: Sandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents de la Peña / James E Crowe / Andrew B Ward /
Abstract: Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV- ...Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.
History
DepositionSep 27, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25011.png

Downloads & links

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Map

FileDownload / File: emd_25011.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map of HKU1 spike with donor 1988 polyclonal Fabs (C1 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 200 pix.
= 412. Å		2.06 Å/pix.
x 200 pix.
= 412. Å		2.06 Å/pix.
x 200 pix.
= 412. 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: 0.02
Minimum - Maximum-0.037389584 - 0.087013654
Average (Standard dev.)0.00017632663 (±0.004240211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 412.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D refined map of MERS spike with donor...

Fileemd_25011_additional_1.map
Annotation3D refined map of MERS spike with donor 1988 polyclonal Fabs (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D refined map of OC43 spike with donor...

Fileemd_25011_additional_2.map
Annotation3D refined map of OC43 spike with donor 1988 polyclonal Fabs (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D refined map of SARS spike with donor...

Fileemd_25011_additional_3.map
Annotation3D refined map of SARS spike with donor 1988 polyclonal Fabs (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D refined map of SARS-2 spike with donor...

Fileemd_25011_additional_4.map
Annotation3D refined map of SARS-2 spike with donor 1988 polyclonal Fabs (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs compl...

EntireName: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Components
  • Complex: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988

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Supramolecule #1: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs compl...

SupramoleculeName: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human coronavirus OC43
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F cells

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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

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 100000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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