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Yorodumi- EMDB-22066: negative stain EM map of SARS-CoV-2 spike in complex with COVA1-12 Fab -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22066 | |||||||||
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Title | negative stain EM map of SARS-CoV-2 spike in complex with COVA1-12 Fab | |||||||||
Map data | negative stain EM map of SARS-CoV-2 spike in complex with COVA1-12 Fab | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 32.0 Å | |||||||||
Authors | Ward AB / Bangaru S / Torres JL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2020 Title: Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Authors: Philip J M Brouwer / Tom G Caniels / Karlijn van der Straten / Jonne L Snitselaar / Yoann Aldon / Sandhya Bangaru / Jonathan L Torres / Nisreen M A Okba / Mathieu Claireaux / Gius Kerster / ...Authors: Philip J M Brouwer / Tom G Caniels / Karlijn van der Straten / Jonne L Snitselaar / Yoann Aldon / Sandhya Bangaru / Jonathan L Torres / Nisreen M A Okba / Mathieu Claireaux / Gius Kerster / Arthur E H Bentlage / Marlies M van Haaren / Denise Guerra / Judith A Burger / Edith E Schermer / Kirsten D Verheul / Niels van der Velde / Alex van der Kooi / Jelle van Schooten / Mariëlle J van Breemen / Tom P L Bijl / Kwinten Sliepen / Aafke Aartse / Ronald Derking / Ilja Bontjer / Neeltje A Kootstra / W Joost Wiersinga / Gestur Vidarsson / Bart L Haagmans / Andrew B Ward / Godelieve J de Bree / Rogier W Sanders / Marit J van Gils / Abstract: The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a large impact on global health, travel, and economy. Therefore, preventative and therapeutic measures are ...The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a large impact on global health, travel, and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent coronavirus disease 2019 (COVID-19) patients using a SARS-CoV-2 stabilized prefusion spike protein. These antibodies had low levels of somatic hypermutation and showed a strong enrichment in VH1-69, VH3-30-3, and VH1-24 gene usage. A subset of the antibodies was able to potently inhibit authentic SARS-CoV-2 infection at a concentration as low as 0.007 micrograms per milliliter. Competition and electron microscopy studies illustrate that the SARS-CoV-2 spike protein contains multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as non-RBD epitopes. In addition to providing guidance for vaccine design, the antibodies described here are promising candidates for COVID-19 treatment and prevention. | |||||||||
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_22066.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-22066-v30.xml emd-22066.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_22066.png | 27 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22066 | HTTPS FTP |
-Validation report
Summary document | emd_22066_validation.pdf.gz | 77.5 KB | Display | EMDB validaton report |
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Full document | emd_22066_full_validation.pdf.gz | 76.6 KB | Display | |
Data in XML | emd_22066_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22066 | 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_22066.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | negative stain EM map of SARS-CoV-2 spike in complex with COVA1-12 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 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-CoV-2 spike in complex with COVA1-12 Fab
Entire | Name: SARS-CoV-2 spike in complex with COVA1-12 Fab |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike in complex with COVA1-12 Fab
Supramolecule | Name: SARS-CoV-2 spike in complex with COVA1-12 Fab / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
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
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 1578 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |