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- EMDB-17849: XBB 1.0 RBD bound to P4J15 (Global) -

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Basic information

Entry
Database: EMDB / ID: EMD-17849
TitleXBB 1.0 RBD bound to P4J15 (Global)
Map dataFull map
Sample
  • Complex: Spike XBB.1 RBD up - P4J15 Fab (Global)
KeywordsSARS-Cov2 / CryoEM / XBB.1 / FAB / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsDuhoo Y / Lau K
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: J Infect / Year: 2023
Title: Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys.
Authors: Craig Fenwick / Priscilla Turelli / Yoan Duhoo / Kelvin Lau / Cécile Herate / Romain Marlin / Myriam Lamrayah / Jérémy Campos / Line Esteves-Leuenberger / Alex Farina / Charlène Raclot / ...Authors: Craig Fenwick / Priscilla Turelli / Yoan Duhoo / Kelvin Lau / Cécile Herate / Romain Marlin / Myriam Lamrayah / Jérémy Campos / Line Esteves-Leuenberger / Alex Farina / Charlène Raclot / Vanessa Genet / Flurin Fiscalini / Julien Cesborn / Laurent Perez / Nathalie Dereuddre-Bosquet / Vanessa Contreras / Kyllian Lheureux / Francis Relouzat / Rana Abdelnabi / Pieter Leyssen / Yves Lévy / Florence Pojer / Roger Le Grand / Didier Trono / Giuseppe Pantaleo /
Abstract: OBJECTIVES: Due to the rapid evolution of SARS-CoV-2 to variants with reduced sensitivity to vaccine-induced humoral immunity and the near complete loss of protective efficacy of licensed therapeutic ...OBJECTIVES: Due to the rapid evolution of SARS-CoV-2 to variants with reduced sensitivity to vaccine-induced humoral immunity and the near complete loss of protective efficacy of licensed therapeutic monoclonal antibodies, we isolated a potent, broad-spectrum neutralizing antibody that could potentially provide prophylactic protection to immunocompromised patient populations.
METHODS: Spike-specific B-cell clones isolated from a vaccinated post-infected donor were profiled for those producing potent neutralizing antibodies against a panel of SARS-CoV-2 variants. The P4J15 ...METHODS: Spike-specific B-cell clones isolated from a vaccinated post-infected donor were profiled for those producing potent neutralizing antibodies against a panel of SARS-CoV-2 variants. The P4J15 antibody was further characterized to define the structural binding epitope, viral resistance, and in vivo efficacy.
RESULTS: The P4J15 mAb shows <20 ng/ml neutralizing activity against all variants including the latest XBB.2.3 and EG.5.1 sub-lineages. Structural studies of P4J15 in complex with Omicron XBB.1 Spike show that the P4J15 epitope shares ∼93% of its buried surface area with the ACE2 contact region, consistent with an ACE2 mimetic antibody. In vitro selection of SARS-CoV-2 mutants escaping P4J15 neutralization showed reduced infectivity, poor ACE2 binding, and mutations are rare in public sequence databases. Using a SARS-CoV-2 XBB.1.5 monkey challenge model, P4J15-LS confers complete prophylactic protection with an exceptionally long in vivo half-life of 43 days.
CONCLUSIONS: The P4J15 mAb has potential as a broad-spectrum anti-SARS-CoV-2 drug for prophylactic protection of at-risk patient populations.
History
DepositionJul 13, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17849.png

Downloads & links

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Map

FileDownload / File: emd_17849.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Voxel sizeX=Y=Z: 1.2681 Å
Density
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.7647968 - 1.4219229
Average (Standard dev.)-0.00036420173 (±0.03170471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 456.51602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17849_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17849_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_17849_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 : Spike XBB.1 RBD up - P4J15 Fab (Global)

EntireName: Spike XBB.1 RBD up - P4J15 Fab (Global)
Components
  • Complex: Spike XBB.1 RBD up - P4J15 Fab (Global)

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Supramolecule #1: Spike XBB.1 RBD up - P4J15 Fab (Global)

SupramoleculeName: Spike XBB.1 RBD up - P4J15 Fab (Global) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Full XBB.1 spike and P4J15-FAB complex. One RBD is up position and 1 FAB is bound to it.
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 490 kDa/nm

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.137 MNaCLSodium chlorideSodium Chloride
0.0027 MKClPotassium Chloride
0.01 MNa2HPO4Sodium Phosphate Dibasic
0.0018 MKH2PO4Potassium Phophate Monobasic
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6769807
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 95910 / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 95910
FSC plot (resolution estimation)

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