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- EMDB-25000: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15 -

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Basic information

Entry
Database: EMDB / ID: EMD-25000
TitleStructure of SARS-CoV-2 spike in complex with polyclonal Fab15
Map dataSharpened map
Sample
  • Complex: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWard AB / Bangaru S / Antanasijevic A
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 26, 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_25000.png

Downloads & links

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Map

FileDownload / File: emd_25000.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 380 pix.
= 397.1 Å		1.05 Å/pix.
x 380 pix.
= 397.1 Å		1.05 Å/pix.
x 380 pix.
= 397.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.02415905 - 0.03872193
Average (Standard dev.)6.429413e-05 (±0.001138732)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 397.09998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_25000_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_25000_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of SARS-CoV-2 spike in complex with polyclonal Fab15

EntireName: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15
Components
  • Complex: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15

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Supramolecule #1: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15

SupramoleculeName: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F cells

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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

Concentration0.7 mg/mL
BufferpH: 7.4 / Component:
ConcentrationFormula
50.0 mMTris-Cl
150.0 mMNaCl
/ Details: TBS 1X
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 5405 / Average exposure time: 7.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 28914
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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