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- EMDB-26367: SARS-2 CoV 6P Mut7 + Fab CC25.52 -

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Basic information

Entry
Database: EMDB / ID: EMD-26367
TitleSARS-2 CoV 6P Mut7 + Fab CC25.52
Map dataSARS-2 CoV 6P Mut7 in complex with Fab CC25.52
Sample
  • Complex: SARS-2 CoV 6P Mut7 ion complex with Fab CC25.52
Keywordsspike protein / coronavirus / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsTorres JL / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Nat Immunol / Year: 2022
Title: Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses.
Authors: Wan-Ting He / Rami Musharrafieh / Ge Song / Katharina Dueker / Longping V Tse / David R Martinez / Alexandra Schäfer / Sean Callaghan / Peter Yong / Nathan Beutler / Jonathan L Torres / ...Authors: Wan-Ting He / Rami Musharrafieh / Ge Song / Katharina Dueker / Longping V Tse / David R Martinez / Alexandra Schäfer / Sean Callaghan / Peter Yong / Nathan Beutler / Jonathan L Torres / Reid M Volk / Panpan Zhou / Meng Yuan / Hejun Liu / Fabio Anzanello / Tazio Capozzola / Mara Parren / Elijah Garcia / Stephen A Rawlings / Davey M Smith / Ian A Wilson / Yana Safonova / Andrew B Ward / Thomas F Rogers / Ralph S Baric / Lisa E Gralinski / Dennis R Burton / Raiees Andrabi /
Abstract: The emergence of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major ...The emergence of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy. Development of broadly effective coronavirus vaccines that can mitigate these threats is needed. Here, we utilized a targeted donor selection strategy to isolate a large panel of human broadly neutralizing antibodies (bnAbs) to sarbecoviruses. Many of these bnAbs are remarkably effective in neutralizing a diversity of sarbecoviruses and against most SARS-CoV-2 VOCs, including the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor-binding domain (RBD). Consistent with targeting of conserved sites, select RBD bnAbs exhibited protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model in vivo. These bnAbs provide new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and provide a molecular basis for effective design of pan-sarbecovirus vaccines.
History
DepositionMar 4, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26367.png

Downloads & links

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Map

FileDownload / File: emd_26367.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-2 CoV 6P Mut7 in complex with Fab CC25.52
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 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: 0.0257
Minimum - Maximum-0.05093719 - 0.099057406
Average (Standard dev.)0.00008853443 (±0.0043879882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26367_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26367_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 : SARS-2 CoV 6P Mut7 ion complex with Fab CC25.52

EntireName: SARS-2 CoV 6P Mut7 ion complex with Fab CC25.52
Components
  • Complex: SARS-2 CoV 6P Mut7 ion complex with Fab CC25.52

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Supramolecule #1: SARS-2 CoV 6P Mut7 ion complex with Fab CC25.52

SupramoleculeName: SARS-2 CoV 6P Mut7 ion complex with Fab CC25.52 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8124
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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