|Entry||Database: EMDB / ID: EMD-22063|
|Title||negative stain EM map of SARS-CoV-2 spike in complex with COVA2-07|
|Sample||SARS-CoV-2 spike in complex with COVA2-07 Fab|
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / Resolution: 28 Å|
|Authors||Ward AB / Bangaru S / Torres JL|
|Funding support|| United States, 1 items |
|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 SARS-CoV-2 has a significant impact on global health, travel and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal ...The rapid spread of SARS-CoV-2 has a significant impact on global health, travel and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated monoclonal antibodies from three convalescent 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 were able to potently inhibit authentic SARS-CoV-2 infection as low as 0.007 μg/mL. 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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_22063.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.06 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire SARS-CoV-2 spike in complex with COVA2-07 Fab
|Entire||Name: SARS-CoV-2 spike in complex with COVA2-07 Fab / Number of components: 1|
-Component #1: protein, SARS-CoV-2 spike in complex with COVA2-07 Fab
|Protein||Name: SARS-CoV-2 spike in complex with COVA2-07 Fab / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human)|
|Specimen||Specimen state: Particle|
|Sample solution||Specimen conc.: 0.02 mg/mL / pH: 7.4|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
Model: Tecnai Spirit / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI SPIRIT|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI EAGLE (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 4359|
|3D reconstruction||Software: RELION / Resolution: 28 Å / Resolution method: FSC 0.5 CUT-OFF|
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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