Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 885.46 kDa 
• Atom Count: 54614 
• Residue Count: 6674 
• Unique protein chains: 1

7JJJ

Structure of SARS-CoV-2 3Q-2P full-length dimers of spike trimers

• DOI: 10.2210/pdb7JJJ/pdb
• EMDataResource: EMD-22354

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


• Deposited: 2020-07-26 Released: 2020-08-26 
• Deposition Author(s): Bangaru, S., Turner, H.L., Ozorowski, G., Antanasijevic, A., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.

Bangaru, S., Ozorowski, G., Turner, H.L., Antanasijevic, A., Huang, D., Wang, X., Torres, J.L., Diedrich, J.K., Tian, J.H., Portnoff, A.D., Patel, N., Massare, M.J., Yates 3rd, J.R., Nemazee, D., Paulson, J.C., Glenn, G., Smith, G., Ward, A.B.

(2020) Science 370: 1089-1094

• PubMed: 33082295 
• DOI: 10.1126/science.abe1502
• Primary Citation of Related Structures:  
  7JJI, 7JJJ


• PubMed Abstract: 
  

Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.

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Related Citations: 

• Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.
  Bangaru, S., Ozorowski, G., Turner, H.L., Antanasijevic, A., Huang, D., Wang, X., Torres, J.L., Diedrich, J.K., Tian, J.H., Portnoff, A.D., Patel, N., Massare, M.J., Yates, J.R., Nemazee, D., Paulson, J.C., Glenn, G., Smith, G., Ward, A.B.
  (2020) Biorxiv --: --

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C, D, E, F	1273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5  Gene Names: S, 2
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	0, 1, 2, 3, 4, 5, 7, 8, 9, AA, BA, CA, DA, EA, FA, G, GA, H, HA, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, SA, T, TA, U, UA, V, VA, W, WA, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, u, v, w, x, y, z	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	6, S	3		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	XA, t	4		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, D, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-07-26 
• Released Date: 2020-08-26 
Deposition Author(s): Bangaru, S., Turner, H.L., Ozorowski, G., Antanasijevic, A., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462

Revision History 

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references