|Entry||Database: EMDB / ID: EMD-22078|
|Title||Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis|
|Sample||Severe acute respiratory syndrome coronavirus 2:|
virus / SARS-CoV-2 spike glycoprotein / ligand
|Function / homology|
Function and homology information
host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell surface receptor binding / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane
Spike glycoprotein S2, coronavirus / Spike receptor binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike receptor binding domain superfamily, coronavirus
|Biological species||Severe acute respiratory syndrome coronavirus 2|
|Method||single particle reconstruction / cryo EM / Resolution: 3.22 Å|
|Authors||Herrera NG / Morano NC / Celikgil A / Georgiev GI / Malonis R / Lee JH / Tong K / Vergnolle O / Massimi A / Yen LY / Noble AJ / Kopylov M / Bonanno JB / Garrett-Thompson SC / Hayes DB / Brenowitz M / Garforth SJ / Eng ET / Lai JR / Almo SC|
|Citation||Journal: bioRxiv / Year: 2020|
Title: Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis.
Authors: Natalia G Herrera / Nicholas C Morano / Alev Celikgil / George I Georgiev / Ryan J Malonis / James H Lee / Karen Tong / Olivia Vergnolle / Aldo B Massimi / Laura Y Yen / Alex J Noble / ...Authors: Natalia G Herrera / Nicholas C Morano / Alev Celikgil / George I Georgiev / Ryan J Malonis / James H Lee / Karen Tong / Olivia Vergnolle / Aldo B Massimi / Laura Y Yen / Alex J Noble / Mykhailo Kopylov / Jeffrey B Bonanno / Sarah C Garrett-Thomson / David B Hayes / Robert H Bortz / Ariel S Wirchnianski / Catalina Florez / Ethan Laudermilch / Denise Haslwanter / J Maximilian Fels / M Eugenia Dieterle / Rohit K Jangra / Jason Barnhill / Amanda Mengotto / Duncan Kimmel / Johanna P Daily / Liise-Anne Pirofski / Kartik Chandran / Michael Brenowitz / Scott J Garforth / Edward T Eng / Jonathan R Lai / Steven C Almo
Abstract: Coronavirus disease 2019 ( ) is a global health crisis caused by the novel severe acute respiratory syndrome coronavirus 2 ( ), and there is a critical need to produce large quantities of high- ...Coronavirus disease 2019 ( ) is a global health crisis caused by the novel severe acute respiratory syndrome coronavirus 2 ( ), and there is a critical need to produce large quantities of high-quality SARS-CoV-2 Spike ( ) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells, two different cell lines selected for increased expression of secreted glycoproteins. We show that ExpiCHO-S cells produce enhanced yields of both SARS-CoV-2 S proteins. Biochemical, biophysical, and structural ( ) characterization of the SARS-CoV-2 S proteins produced in both cell lines demonstrate that the reported purification strategy yields high quality S protein (non-aggregated, uniform material with appropriate biochemical and biophysical properties). Importantly, we show that multiple preparations of these two recombinant S proteins from either cell line exhibit identical behavior in two different serology assays. We also evaluate the specificity of S protein-mediated host cell binding by examining interactions with proposed binding partners in the human secretome. In addition, the antigenicity of these proteins is demonstrated by standard ELISAs, and in a flexible protein microarray format. Collectively, we establish an array of metrics for ensuring the production of high-quality S protein to support clinical, biological, biochemical, structural and mechanistic studies to combat the global pandemic caused by SARS-CoV-2.
|Validation Report||PDB-ID: 6x6p|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_22078.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.058 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Severe acute respiratory syndrome coronavirus 2
|Entire||Name: Severe acute respiratory syndrome coronavirus 2 / Number of components: 3|
-Component #1: virus, Severe acute respiratory syndrome coronavirus 2
|Virus||Name: Severe acute respiratory syndrome coronavirus 2 / Class: VIRION / Empty: Yes / Enveloped: Yes / Isolate: OTHER|
|Species||Species: Severe acute respiratory syndrome coronavirus 2|
|Source (engineered)||Expression System: Cricetulus griseus (Chinese hamster)|
-Component #2: protein, SARS-CoV-2 spike glycoprotein
|Protein||Name: SARS-CoV-2 spike glycoprotein / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 140.824406 kDa|
|Source||Species: Severe acute respiratory syndrome coronavirus 2|
|Source (engineered)||Expression System: Cricetulus griseus (Chinese hamster)|
-Component #3: ligand, N-ACETYL-D-GLUCOSAMINE
|Ligand||Name: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 57 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1 mg/mL / pH: 8|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 %|
-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: 66.5 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2500.0 nm|
|Specimen Holder||Model: OTHER|
|Image acquisition||Number of digital images: 1131|
|Processing||Method: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 54395|
|3D reconstruction||Software: cryoSPARC / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
-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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