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- EMDB-24895: Ab20 in complex with SARS-CoV-2 spike (6P) -

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Basic information

Entry
Database: EMDB / ID: EMD-24895
TitleAb20 in complex with SARS-CoV-2 spike (6P)
Map dataAb20 in complex with SARS-CoV-2 spike
Sample
  • Complex: Ab16 Fab in complex with SARS-CoV-2 Spike (6P)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsWindsor IW / Hauser BM / Schmidt AG
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146779 United States
Other governmentMassachusetts Consortium on Pathogenesis Readiness (MassCPR) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007753 United States
CitationJournal: bioRxiv / Year: 2021
Title: Rationally designed immunogens enable immune focusing to the SARS-CoV-2 receptor binding motif.
Authors: Blake M Hauser / Maya Sangesland / Kerri J St Denis / Ian W Windsor / Jared Feldman / Evan C Lam / Ty Kannegieter / Alejandro B Balazs / Daniel Lingwood / Aaron G Schmidt
Abstract: Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help ...Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help reduce the likelihood of viral escape and aid in preventing the spread of related viruses with pandemic potential. One such functionally conserved viral epitope is the site to which a receptor must bind to facilitate viral entry. Here, we leveraged rational immunogen design strategies to focus humoral responses to the receptor binding motif (RBM) on the SARS-CoV-2 spike. Using glycan engineering and epitope scaffolding, we find an improved targeting of the serum response to the RBM in context of SARS-CoV-2 spike imprinting. Furthermore, we observed a robust SARS-CoV-2-neutralizing serum response with increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses and represents an adaptable design approach for targeting conserved epitopes on other viral glycoproteins.
ONE SENTENCE SUMMARY: SARS-CoV-2 immune focusing with engineered immunogens.
History
DepositionSep 17, 2021-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24895.png

Downloads & links

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Map

FileDownload / File: emd_24895.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAb20 in complex with SARS-CoV-2 spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 300 pix.
= 339. Å		1.13 Å/pix.
x 300 pix.
= 339. Å		1.13 Å/pix.
x 300 pix.
= 339. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.026509797 - 0.048028402
Average (Standard dev.)0.0002301781 (±0.0016524284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 339.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ab16 Fab in complex with SARS-CoV-2 Spike (6P)

EntireName: Ab16 Fab in complex with SARS-CoV-2 Spike (6P)
Components
  • Complex: Ab16 Fab in complex with SARS-CoV-2 Spike (6P)

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Supramolecule #1: Ab16 Fab in complex with SARS-CoV-2 Spike (6P)

SupramoleculeName: Ab16 Fab in complex with SARS-CoV-2 Spike (6P) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8761
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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