+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31434 | |||||||||
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Title | SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / RBD / Fab / Cocktail / VIRUS / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Dou Y / Wang X / Liu P / Lu B / Wang K | |||||||||
Funding support | 1 items
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Citation | Journal: Antib Ther / Year: 2023 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31434.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-31434-v30.xml emd-31434.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
Images | emd_31434.png | 62.4 KB | ||
Filedesc metadata | emd-31434.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31434 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31434 | HTTPS FTP |
-Validation report
Summary document | emd_31434_validation.pdf.gz | 427 KB | Display | EMDB validaton report |
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Full document | emd_31434_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | emd_31434_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_31434_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31434 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31434 | HTTPS FTP |
-Related structure data
Related structure data | 7f3qMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31434.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : SARS-CoV-2 S protein RBD in complex with two Fabs
+Supramolecule #1: SARS-CoV-2 S protein RBD in complex with two Fabs
+Supramolecule #2: SARS-CoV-2 S protein RBD
+Supramolecule #3: FAB
+Macromolecule #1: Spike glycoprotein
+Macromolecule #2: Heavy chain of A34-2 Fab
+Macromolecule #3: Light chain of A34-2 Fab
+Macromolecule #4: Heavy chain of A5-10 Fab
+Macromolecule #5: Light chain of A5-10 Fab
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #7: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 401023 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |