+Open data
-Basic information
Entry | Database: PDB / ID: 7q0a | ||||||||||||
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Title | SARS-CoV-2 Spike ectodomain with Fab FI3A | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV2 / Spike / ectodomain / fab / antibody / trimer / virus | ||||||||||||
Function / homology | Function and homology information : / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...: / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / membrane => GO:0016020 / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Bat coronavirus Rp3/2004 Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||
Authors | Duyvesteyn, H.M.E. / Ren, J. / Stuart, D.I. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Theranostics / Year: 2022 Title: Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2. Authors: Kuan-Ying A Huang / Daming Zhou / Tiong Kit Tan / Charles Chen / Helen M E Duyvesteyn / Yuguang Zhao / Helen M Ginn / Ling Qin / Pramila Rijal / Lisa Schimanski / Robert Donat / Adam Harding ...Authors: Kuan-Ying A Huang / Daming Zhou / Tiong Kit Tan / Charles Chen / Helen M E Duyvesteyn / Yuguang Zhao / Helen M Ginn / Ling Qin / Pramila Rijal / Lisa Schimanski / Robert Donat / Adam Harding / Javier Gilbert-Jaramillo / William James / Julia A Tree / Karen Buttigieg / Miles Carroll / Sue Charlton / Chia-En Lien / Meei-Yun Lin / Cheng-Pin Chen / Shu-Hsing Cheng / Xiaorui Chen / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Che Ma / Alain R Townsend / David I Stuart / Abstract: Administration of potent anti-receptor-binding domain (RBD) monoclonal antibodies has been shown to curtail viral shedding and reduce hospitalization in patients with SARS-CoV-2 infection. However, ... Administration of potent anti-receptor-binding domain (RBD) monoclonal antibodies has been shown to curtail viral shedding and reduce hospitalization in patients with SARS-CoV-2 infection. However, the structure-function analysis of potent human anti-RBD monoclonal antibodies and its links to the formulation of antibody cocktails remains largely elusive. Previously, we isolated a panel of neutralizing anti-RBD monoclonal antibodies from convalescent patients and showed their neutralization efficacy . Here, we elucidate the mechanism of action of antibodies and dissect antibodies at the epitope level, which leads to a formation of a potent antibody cocktail. We found that representative antibodies which target non-overlapping epitopes are effective against wild type virus and recently emerging variants of concern, whilst being encoded by antibody genes with few somatic mutations. Neutralization is associated with the inhibition of binding of viral RBD to ACE2 and possibly of the subsequent fusion process. Structural analysis of representative antibodies, by cryo-electron microscopy and crystallography, reveals that they have some unique aspects that are of potential value while sharing some features in common with previously reported neutralizing monoclonal antibodies. For instance, one has a common VH 3-53 public variable region yet is unusually resilient to mutation at residue 501 of the RBD. We evaluate the efficacy of an antibody cocktail consisting of two potent non-competing anti-RBD antibodies in a Syrian hamster model. We demonstrate that the cocktail prevents weight loss, reduces lung viral load and attenuates pulmonary inflammation in hamsters in both prophylactic and therapeutic settings. Although neutralization of one of these antibodies is abrogated by the mutations of variant B.1.351, it is also possible to produce a bi-valent cocktail of antibodies both of which are resilient to variants B.1.1.7, B.1.351 and B.1.617.2. These findings support the up-to-date and rational design of an anti-RBD antibody cocktail as a therapeutic candidate against COVID-19. | ||||||||||||
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 | 7q0a.cif.gz | 580.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q0a.ent.gz | 480.9 KB | Display | PDB format |
PDBx/mmJSON format | 7q0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q0a_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7q0a_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7q0a_validation.xml.gz | 70.5 KB | Display | |
Data in CIF | 7q0a_validation.cif.gz | 102 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/7q0a ftp://data.pdbj.org/pub/pdb/validation_reports/q0/7q0a | HTTPS FTP |
-Related structure data
Related structure data | 13742MC 7pqyC 7pqzC 7pr0C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 145856.078 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Bat coronavirus Rp3/2004 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2, UniProt: Q3I5J5 #2: Antibody | | Mass: 12622.150 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: 11604.820 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) #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-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 |
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Molecular weight | Value: 21776.381 kDa/nm | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 4.6 | ||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 47.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9095 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7ND5 |