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- EMDB-41075: SARS-CoV-2 spike in complex with Fab 71281-33 -

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Basic information

Entry
Database: EMDB / ID: EMD-41075
TitleSARS-CoV-2 spike in complex with Fab 71281-33
Map data
Sample
  • Complex: Cov2 spike in complex with Fab 71281-33
    • Complex: Cov2-spike
    • Complex: FabFragment antigen-binding
Keywordsviral-protein / fab / IMMUNE complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011-18-2-0001 United States
CitationJournal: Cell Rep Med / Year: 2023
Title: SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes.
Authors: Steven C Wall / Naveenchandra Suryadevara / Changil Kim / Andrea R Shiakolas / Clinton M Holt / Emma B Irbe / Perry T Wasdin / Yukthi P Suresh / Elad Binshtein / Elaine C Chen / Seth J Zost ...Authors: Steven C Wall / Naveenchandra Suryadevara / Changil Kim / Andrea R Shiakolas / Clinton M Holt / Emma B Irbe / Perry T Wasdin / Yukthi P Suresh / Elad Binshtein / Elaine C Chen / Seth J Zost / Elizabeth Canfield / James E Crowe / Mary Ann Thompson-Arildsen / Daniel J Sheward / Robert H Carnahan / Ivelin S Georgiev /
Abstract: From the beginning of the COVID-19 pandemic, children have exhibited different susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, reinfection, and disease ...From the beginning of the COVID-19 pandemic, children have exhibited different susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, reinfection, and disease compared with adults. Motivated by the established significance of SARS-CoV-2-neutralizing antibodies in adults, here we characterize SARS-CoV-2-specific antibody repertoires in a young cohort of individuals aged from 5 months to 18 years old. Our results show that neutralizing antibodies in children possess similar genetic features compared to antibodies identified in adults, with multiple antibodies from children belonging to previously established public antibody clonotypes in adults. Notably, antibodies from children show potent neutralization of circulating SARS-CoV-2 variants that have cumulatively resulted in resistance to virtually all approved monoclonal antibody therapeutics. Our results show that children can rely on similar SARS-CoV-2 antibody neutralization mechanisms compared to adults and are an underutilized source for the discovery of effective antibody therapeutics to counteract the ever-evolving pandemic.
History
DepositionJun 16, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41075.png

Downloads & links

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Map

FileDownload / File: emd_41075.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.36 Å
Density
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-4.587879 - 12.033949
Average (Standard dev.)-0.039356217 (±0.5100627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41075_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41075_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cov2 spike in complex with Fab 71281-33

EntireName: Cov2 spike in complex with Fab 71281-33
Components
  • Complex: Cov2 spike in complex with Fab 71281-33
    • Complex: Cov2-spike
    • Complex: FabFragment antigen-binding

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Supramolecule #1: Cov2 spike in complex with Fab 71281-33

SupramoleculeName: Cov2 spike in complex with Fab 71281-33 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Cov2-spike

SupramoleculeName: Cov2-spike / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Fab

SupramoleculeName: Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

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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

Concentration0.01 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: uranyl formate
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 247 / Average exposure time: 1.0 sec. / Average electron dose: 33.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 7003

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Atomic model buiding 1

RefinementSpace: REAL

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