+Open data
-Basic information
Entry | Database: PDB / ID: 7phg | ||||||
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Title | MaP OF P5C3RBD Interface | ||||||
Components |
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Keywords | VIRAL PROTEIN / RBD / antibody | ||||||
Function / homology | Surface glycoprotein Function and homology information | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Perez, L. | ||||||
Citation | Journal: Cell Rep / Year: 2021 Title: A highly potent antibody effective against SARS-CoV-2 variants of concern. Authors: Craig Fenwick / Priscilla Turelli / Laurent Perez / Céline Pellaton / Line Esteves-Leuenberger / Alex Farina / Jérémy Campos / Erica Lana / Flurin Fiscalini / Charlène Raclot / Florence ...Authors: Craig Fenwick / Priscilla Turelli / Laurent Perez / Céline Pellaton / Line Esteves-Leuenberger / Alex Farina / Jérémy Campos / Erica Lana / Flurin Fiscalini / Charlène Raclot / Florence Pojer / Kelvin Lau / Davide Demurtas / Marc Descatoire / Victor S Joo / Mathilde Foglierini / Alessandra Noto / Rana Abdelnabi / Caroline S Foo / Laura Vangeel / Johan Neyts / Wenjuan Du / Berend-Jan Bosch / Geertruida Veldman / Pieter Leyssen / Volker Thiel / Roger LeGrand / Yves Lévy / Didier Trono / Giuseppe Pantaleo / Abstract: Control of the ongoing SARS-CoV-2 pandemic is endangered by the emergence of viral variants with increased transmission efficiency, resistance to marketed therapeutic antibodies, and reduced ...Control of the ongoing SARS-CoV-2 pandemic is endangered by the emergence of viral variants with increased transmission efficiency, resistance to marketed therapeutic antibodies, and reduced sensitivity to vaccine-induced immunity. Here, we screen B cells from COVID-19 donors and identify P5C3, a highly potent and broadly neutralizing monoclonal antibody with picomolar neutralizing activity against all SARS-CoV-2 variants of concern (VOCs) identified to date. Structural characterization of P5C3 Fab in complex with the spike demonstrates a neutralizing activity defined by a large buried surface area, highly overlapping with the receptor-binding domain (RBD) surface necessary for ACE2 interaction. We further demonstrate that P5C3 shows complete prophylactic protection in the SARS-CoV-2-infected hamster challenge model. These results indicate that P5C3 opens exciting perspectives either as a prophylactic agent in immunocompromised individuals with poor response to vaccination or as combination therapy in SARS-CoV-2-infected individuals. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7phg.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7phg.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 7phg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7phg_validation.pdf.gz | 516.8 KB | Display | wwPDB validaton report |
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Full document | 7phg_full_validation.pdf.gz | 524.9 KB | Display | |
Data in XML | 7phg_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7phg_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/7phg ftp://data.pdbj.org/pub/pdb/validation_reports/ph/7phg | HTTPS FTP |
-Related structure data
Related structure data | 13415MC 7p40C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 21986.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A7S6Y2X1 |
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#2: Antibody | Mass: 13339.821 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#3: Antibody | Mass: 11728.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RBD fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) |
Buffer solution | pH: 7.3 |
Buffer component | Formula: PBS |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: HELIUM |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 585005 / Symmetry type: POINT |