|Entry||Database: EMDB / ID: EMD-30277|
|Title||Cryo EM map of the interface between NTD of SARS-CoV-2 and 4A8|
|Sample||interface between NTD of SARS-CoV-2 and 4A8|
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.3 Å|
|Authors||Yan RH / Zhang YY / Guo YY / Li YN / Xia L / Zhou Q|
|Funding support|| China, 3 items |
|Citation||Journal: Science / Year: 2020|
Title: A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2.
Authors: Xiangyang Chi / Renhong Yan / Jun Zhang / Guanying Zhang / Yuanyuan Zhang / Meng Hao / Zhe Zhang / Pengfei Fan / Yunzhu Dong / Yilong Yang / Zhengshan Chen / Yingying Guo / Jinlong Zhang / ...Authors: Xiangyang Chi / Renhong Yan / Jun Zhang / Guanying Zhang / Yuanyuan Zhang / Meng Hao / Zhe Zhang / Pengfei Fan / Yunzhu Dong / Yilong Yang / Zhengshan Chen / Yingying Guo / Jinlong Zhang / Yaning Li / Xiaohong Song / Yi Chen / Lu Xia / Ling Fu / Lihua Hou / Junjie Xu / Changming Yu / Jianmin Li / Qiang Zhou / Wei Chen /
Abstract: Developing therapeutics against SARS-CoV-2 could be guided by the distribution of epitopes, not only on the receptor binding domain (RBD) of the Spike (S) protein, but also across the full Spike (S) ...Developing therapeutics against SARS-CoV-2 could be guided by the distribution of epitopes, not only on the receptor binding domain (RBD) of the Spike (S) protein, but also across the full Spike (S) protein. We isolated and characterized monoclonal antibodies (mAbs) from ten convalescent COVID-19 patients. Three mAbs showed neutralizing activities against authentic SARS-CoV-2. An mAb, named 4A8, exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2, but does not bind the RBD. We defined the epitope of 4A8 as the N terminal domain (NTD) of the S protein by determining its cryo-EM structure in complex with the S protein to an overall resolution of 3.1 Angstrom and local resolution of 3.3 Angstrom for the 4A8-NTD interface. This points to the NTD as a promising target for therapeutic mAbs against COVID-19.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_30277.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.087 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire interface between NTD of SARS-CoV-2 and 4A8
|Entire||Name: interface between NTD of SARS-CoV-2 and 4A8 / Number of components: 1|
-Component #1: protein, interface between NTD of SARS-CoV-2 and 4A8
|Protein||Name: interface between NTD of SARS-CoV-2 and 4A8 / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Processing||Method: single particle reconstruction / Number of projections: 217743|
|3D reconstruction||Software: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 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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