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Yorodumi- EMDB-23525: SARS-2 CoV 6P Mut 7 in complex with fragment antigen binding (fab) I14 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23525 | |||||||||
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Title | SARS-2 CoV 6P Mut 7 in complex with fragment antigen binding (fab) I14 | |||||||||
Map data | SARS-2 CoV 6P Mut 7 in complex with fragment antigen binding (Fab) I14 | |||||||||
Sample |
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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 / Attachment and Entry / membrane fusion / 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 | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 29.0 Å | |||||||||
Authors | Torres JL / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2021 Title: Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Authors: Emanuele Andreano / Emanuele Nicastri / Ida Paciello / Piero Pileri / Noemi Manganaro / Giulia Piccini / Alessandro Manenti / Elisa Pantano / Anna Kabanova / Marco Troisi / Fabiola Vacca / ...Authors: Emanuele Andreano / Emanuele Nicastri / Ida Paciello / Piero Pileri / Noemi Manganaro / Giulia Piccini / Alessandro Manenti / Elisa Pantano / Anna Kabanova / Marco Troisi / Fabiola Vacca / Dario Cardamone / Concetta De Santi / Jonathan L Torres / Gabriel Ozorowski / Linda Benincasa / Hyesun Jang / Cecilia Di Genova / Lorenzo Depau / Jlenia Brunetti / Chiara Agrati / Maria Rosaria Capobianchi / Concetta Castilletti / Arianna Emiliozzi / Massimiliano Fabbiani / Francesca Montagnani / Luisa Bracci / Giuseppe Sautto / Ted M Ross / Emanuele Montomoli / Nigel Temperton / Andrew B Ward / Claudia Sala / Giuseppe Ippolito / Rino Rappuoli / Abstract: Human monoclonal antibodies are safe, preventive, and therapeutic tools that can be rapidly developed to help restore the massive health and economic disruption caused by the coronavirus disease 2019 ...Human monoclonal antibodies are safe, preventive, and therapeutic tools that can be rapidly developed to help restore the massive health and economic disruption caused by the coronavirus disease 2019 (COVID-19) pandemic. By single-cell sorting 4,277 SARS-CoV-2 spike protein-specific memory B cells from 14 COVID-19 survivors, 453 neutralizing antibodies were identified. The most potent neutralizing antibodies recognized the spike protein receptor-binding domain, followed in potency by antibodies that recognize the S1 domain, the spike protein trimer, and the S2 subunit. Only 1.4% of them neutralized the authentic virus with a potency of 1-10 ng/mL. The most potent monoclonal antibody, engineered to reduce the risk of antibody-dependent enhancement and prolong half-life, neutralized the authentic wild-type virus and emerging variants containing D614G, E484K, and N501Y substitutions. Prophylactic and therapeutic efficacy in the hamster model was observed at 0.25 and 4 mg/kg respectively in absence of Fc functions. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23525.map.gz | 49.1 MB | EMDB map data format | |
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Header (meta data) | emd-23525-v30.xml emd-23525.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_23525.png | 33.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23525 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23525 | HTTPS FTP |
-Validation report
Summary document | emd_23525_validation.pdf.gz | 291.3 KB | Display | EMDB validaton report |
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Full document | emd_23525_full_validation.pdf.gz | 290.8 KB | Display | |
Data in XML | emd_23525_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_23525_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23525 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23525 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23525.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SARS-2 CoV 6P Mut 7 in complex with fragment antigen binding (Fab) I14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS-2 CoV 6P Mut7 Spike Protein in complex with Fab J08
Entire | Name: SARS-2 CoV 6P Mut7 Spike Protein in complex with Fab J08 |
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Components |
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-Supramolecule #1: SARS-2 CoV 6P Mut7 Spike Protein in complex with Fab J08
Supramolecule | Name: SARS-2 CoV 6P Mut7 Spike Protein in complex with Fab J08 type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: fragment antigent binding (Fab) I14
Supramolecule | Name: fragment antigent binding (Fab) I14 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: SARS-2 CoV 6P Mut7 Spike Protein
Supramolecule | Name: SARS-2 CoV 6P Mut7 Spike Protein / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: 2% |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 8229 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |