6X6P

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis

• PDB DOI:  https://doi.org/10.2210/pdb6X6P/pdb
• EM Map EMD-22078: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2020-05-28 Released: 2020-06-10 
• Deposition Author(s): Herrera, N.G., Morano, N.C., Celikgil, A., Georgiev, G.I., Malonis, R., Lee, J.H., Tong, K., Vergnolle, O., Massimi, A., Yen, L.Y., Noble, A.J., Kopylov, M., Bonanno, J.B., Garrett-Thompson, S.C., Hayes, D.B., Brenowitz, M., Garforth, S.J., Eng, E.T., Lai, J.R., Almo, S.C.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis.

Herrera, N.G., Morano, N.C., Celikgil, A., Georgiev, G.I., Malonis, R.J., Lee, J.H., Tong, K., Vergnolle, O., Massimi, A.B., Yen, L.Y., Noble, A.J., Kopylov, M., Bonanno, J.B., Garrett-Thomson, S.C., Hayes, D.B., Bortz, R.H., Wirchnianski, A.S., Florez, C., Laudermilch, E., Haslwanter, D., Fels, J.M., Dieterle, M.E., Jangra, R.K., Barnhill, J., Mengotto, A., Kimmel, D., Daily, J.P., Pirofski, L.A., Chandran, K., Brenowitz, M., Garforth, S.J., Eng, E.T., Lai, J.R., Almo, S.C.

(2020) Biorxiv 

• PubMed: 32587972 
• DOI: https://doi.org/10.1101/2020.06.14.150607
• Primary Citation of Related Structures:  
  6X6P


• PubMed Abstract: 
  

Coronavirus disease 2019 ( COVID-19 ) is a global health crisis caused by the novel severe acute respiratory syndrome coronavirus 2 ( SARS-CoV-2 ), and there is a critical need to produce large quantities of high-quality SARS-CoV-2 Spike ( S ) 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 ( cryo-EM ) 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.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY, 10461, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 434.87 kDa 
• Atom Count: 24,615 
• Modelled Residue Count: 3,051 
• Deposited Residue Count: 3,822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,274	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H, I, J, K, L, M, N, O	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth C], MA [auth C], NA [auth C], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18-3845
RECONSTRUCTION	cryoSPARC	2.14.2

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Herrera, N.G., Morano, N.C., Celikgil, A., Georgiev, G.I., Malonis, R., Lee, J.H., Tong, K., Vergnolle, O., Massimi, A., Yen, L.Y., Noble, A.J., Kopylov, M., Bonanno, J.B., Garrett-Thompson, S.C., Hayes, D.B., Brenowitz, M., Garforth, S.J., Eng, E.T., Lai, J.R., Almo, S.C.

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-01-27
  Changes: Refinement description, Structure summary