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Open data
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Basic information
Entry | Database: PDB / ID: 7f3q | ||||||
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Title | SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / RBD / Fab / Cocktail / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 ...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 / 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 | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Dou, Y. / Wang, X. / Liu, P. / Lu, B. / Wang, K. | ||||||
Funding support | 1items
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![]() | ![]() Title: Development of neutralizing antibodies against SARS-CoV-2, using a high-throughput single-B-cell cloning method. Authors: Yang Dou / Ke Xu / Yong-Qiang Deng / Zijing Jia / Jun Lan / Xiaoyu Xu / Guorui Zhang / Tianshu Cao / Pan Liu / Xiangxi Wang / Xinquan Wang / Lingjie Xu / Pan Du / Cheng-Feng Qin / Hong Liu / ...Authors: Yang Dou / Ke Xu / Yong-Qiang Deng / Zijing Jia / Jun Lan / Xiaoyu Xu / Guorui Zhang / Tianshu Cao / Pan Liu / Xiangxi Wang / Xinquan Wang / Lingjie Xu / Pan Du / Cheng-Feng Qin / Hong Liu / Yafeng Li / Guizhen Wu / Kang Wang / Bai Lu / ![]() Abstract: BACKGROUND: Rapid and efficient strategies are needed to discover neutralizing antibodies (nAbs) from B cells derived from virus-infected patients. METHODS: Here, we report a high-throughput single-B-cell cloning method for high-throughput isolation of nAbs targeting diverse epitopes on the SARS-CoV-2-RBD (receptor binding domain) from ...METHODS: Here, we report a high-throughput single-B-cell cloning method for high-throughput isolation of nAbs targeting diverse epitopes on the SARS-CoV-2-RBD (receptor binding domain) from convalescent COVID-19 patients. This method is simple, fast and highly efficient in generating SARS-CoV-2-neutralizing antibodies from COVID-19 patients' B cells. RESULTS: Using this method, we have developed multiple nAbs against distinct SARS-CoV-2-RBD epitopes. CryoEM and crystallography revealed precisely how they bind RBD. In live virus assay, these nAbs ...RESULTS: Using this method, we have developed multiple nAbs against distinct SARS-CoV-2-RBD epitopes. CryoEM and crystallography revealed precisely how they bind RBD. In live virus assay, these nAbs are effective in blocking viral entry to the host cells. CONCLUSION: This simple and efficient method may be useful in developing human therapeutic antibodies for other diseases and next pandemic. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.1 KB | Display | ![]() |
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PDB format | ![]() | 160.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 905.9 KB | Display | ![]() |
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Full document | ![]() | 921.7 KB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31434MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Antibody , 4 types, 4 molecules HLCB
#2: Antibody | Mass: 23326.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 22769.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Antibody | Mass: 24014.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Antibody | Mass: 22182.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars / Non-polymers , 3 types, 3 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/MES.gif)
#1: Protein | Mass: 141297.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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#6: Sugar | ChemComp-NAG / |
#7: Chemical | ChemComp-MES / |
-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 401023 / Symmetry type: POINT |