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Yorodumi- PDB-7yc5: Cryo-EM structure of SARS-CoV-2 spike in complex with K202.B bisp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yc5 | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike in complex with K202.B bispecific antibody | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / spike protein / antibody / bispecific antibody / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Yoo, Y. / Cho, H.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Antiviral Res / Year: 2023 Title: Novel bispecific human antibody platform specifically targeting a fully open spike conformation potently neutralizes multiple SARS-CoV-2 variants. Authors: Ji Woong Kim / Kyun Heo / Hyun Jung Kim / Youngki Yoo / Hyun-Soo Cho / Hui Jeong Jang / Ho-Young Lee / In Young Ko / Ju Rang Woo / Yea Bin Cho / Ji Hyun Lee / Ha Rim Yang / Ha Gyeong Shin / ...Authors: Ji Woong Kim / Kyun Heo / Hyun Jung Kim / Youngki Yoo / Hyun-Soo Cho / Hui Jeong Jang / Ho-Young Lee / In Young Ko / Ju Rang Woo / Yea Bin Cho / Ji Hyun Lee / Ha Rim Yang / Ha Gyeong Shin / Hye Lim Choi / Kyusang Hwang / Sokho Kim / Hanseong Kim / Kwangrok Chun / Sukmook Lee / Abstract: Rapid emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted an urgent need for the development of broadly applicable and potently neutralizing ...Rapid emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted an urgent need for the development of broadly applicable and potently neutralizing antibody platform against the SARS-CoV-2, which can be used for combatting the coronavirus disease 2019 (COVID-19). In this study, based on a noncompeting pair of phage display-derived human monoclonal antibodies (mAbs) specific to the receptor-binding domain (RBD) of SARS-CoV-2 isolated from human synthetic antibody library, we generated K202.B, a novel engineered bispecific antibody with an immunoglobulin G4-single-chain variable fragment design, with sub- or low nanomolar antigen-binding avidity. Compared with the parental mAbs or mAb cocktail, the K202.B antibody showed superior neutralizing potential against a variety of SARS-CoV-2 variants in vitro. Furthermore, structural analysis of bispecific antibody-antigen complexes using cryo-electron microscopy revealed the mode of action of K202.B complexed with a fully open three-RBD-up conformation of SARS-CoV-2 trimeric spike proteins by simultaneously interconnecting two independent epitopes of the SARS-CoV-2 RBD via inter-protomer interactions. Intravenous monotherapy using K202.B exhibited potent neutralizing activity in SARS-CoV-2 wild-type- and B.1.617.2 variant-infected mouse models, without significant toxicity in vivo. The results indicate that this novel approach of development of immunoglobulin G4-based bispecific antibody from an established human recombinant antibody library is likely to be an effective strategy for the rapid development of bispecific antibodies, and timely management against fast-evolving SARS-CoV-2 variants. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yc5.cif.gz | 1016.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yc5.ent.gz | 793.8 KB | Display | PDB format |
PDBx/mmJSON format | 7yc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yc5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7yc5_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7yc5_validation.xml.gz | 149 KB | Display | |
Data in CIF | 7yc5_validation.cif.gz | 220.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/7yc5 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/7yc5 | HTTPS FTP |
-Related structure data
Related structure data | 33734MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 133781.312 Da / Num. of mol.: 3 Mutation: R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2 #2: Antibody | Mass: 49646.191 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 49846.777 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) #4: 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
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | 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: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 600 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1086347 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182595 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE |