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- EMDB-25498: CV3-25 IgG in complex with SARS-CoV-2 6P-D614G S protein -

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Basic information

Entry
Database: EMDB / ID: EMD-25498
TitleCV3-25 IgG in complex with SARS-CoV-2 6P-D614G S protein
Map dataCV3-25 IgG in complex with SARS-CoV-2 6P-D614G S protein
Sample
  • Complex: CV3-25 IgG + SARS-CoV-2 6P-D614G S Protein
    • Complex: SARS-CoV-2 6P-D614G S Protein
    • Complex: CV3-25 IgG
KeywordsCV3-25 / SARS-CoV-2 / SARS2 / monoclonal / nsEM / S2 stem / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 33.0 Å
AuthorsJackson AM / Ozorowski G / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.
Authors: Nicholas K Hurlburt / Leah J Homad / Irika Sinha / Madeleine F Jennewein / Anna J MacCamy / Yu-Hsin Wan / Jim Boonyaratanakornkit / Anton M Sholukh / Abigail M Jackson / Panpan Zhou / Dennis ...Authors: Nicholas K Hurlburt / Leah J Homad / Irika Sinha / Madeleine F Jennewein / Anna J MacCamy / Yu-Hsin Wan / Jim Boonyaratanakornkit / Anton M Sholukh / Abigail M Jackson / Panpan Zhou / Dennis R Burton / Raiees Andrabi / Gabriel Ozorowski / Andrew B Ward / Leonidas Stamatatos / Marie Pancera / Andrew T McGuire /
Abstract: Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread ...Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks could occur. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-CoV protection. We previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 spike, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and binds to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is maintained against the Alpha, Delta, Gamma and Omicron variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region. Negative stain electron microscopy and a 1.74 Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs.
History
DepositionNov 22, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25498.png

Downloads & links

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Map

FileDownload / File: emd_25498.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCV3-25 IgG in complex with SARS-CoV-2 6P-D614G S protein
Voxel sizeX=Y=Z: 2.06 Å
Density
Contour LevelBy AUTHOR: 0.00596
Minimum - Maximum-0.026021883 - 0.07720041
Average (Standard dev.)0.00000028257332 (±0.0022339798)
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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Sample components

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Entire : CV3-25 IgG + SARS-CoV-2 6P-D614G S Protein

EntireName: CV3-25 IgG + SARS-CoV-2 6P-D614G S Protein
Components
  • Complex: CV3-25 IgG + SARS-CoV-2 6P-D614G S Protein
    • Complex: SARS-CoV-2 6P-D614G S Protein
    • Complex: CV3-25 IgG

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Supramolecule #1: CV3-25 IgG + SARS-CoV-2 6P-D614G S Protein

SupramoleculeName: CV3-25 IgG + SARS-CoV-2 6P-D614G S Protein / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: SARS-CoV-2 6P-D614G S Protein

SupramoleculeName: SARS-CoV-2 6P-D614G S Protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: CV3-25 IgG

SupramoleculeName: CV3-25 IgG / type: complex / ID: 3 / Parent: 1
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: Nano-W (Nanoprobes)
GridModel: Homemade / Material: COPPER / Mesh: 400

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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 magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2499
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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