7Q1Z | pdb_00007q1z

Structure of formaldehyde cross-linked SARS-CoV-2 S glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb7Q1Z/pdb
• EM Map EMD-13776: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-10-22 Released: 2022-03-09 
• Deposition Author(s): Sulbaran, G., Effantin, G., Schoehn, G., Weissenhorn, W.
• Funding Organization(s): European Union (EU), Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection.

Sulbaran, G., Maisonnasse, P., Amen, A., Effantin, G., Guilligay, D., Dereuddre-Bosquet, N., Burger, J.A., Poniman, M., Grobben, M., Buisson, M., Dergan Dylon, S., Naninck, T., Lemaitre, J., Gros, W., Gallouet, A.S., Marlin, R., Bouillier, C., Contreras, V., Relouzat, F., Fenel, D., Thepaut, M., Bally, I., Thielens, N., Fieschi, F., Schoehn, G., van der Werf, S., van Gils, M.J., Sanders, R.W., Poignard, P., Le Grand, R., Weissenhorn, W.

(2022) Cell Rep Med 3: 100528-100528

• PubMed: 35233549 
• DOI: https://doi.org/10.1016/j.xcrm.2022.100528
• Primary Citation Related Structures: 
  7Q1Z


• PubMed Abstract: 
  

  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused an ongoing global health crisis. Here, we present as a vaccine candidate synthetic SARS-CoV-2 spike (S) glycoprotein-coated lipid vesicles that resemble virus-like particles. Soluble S glycoprotein trimer stabilization by formaldehyde cross-linking introduces two major inter-protomer cross-links that keep all receptor-binding domains in the "down" conformation. Immunization of cynomolgus macaques with S coated onto lipid vesicles (S-LVs) induces high antibody titers with potent neutralizing activity against the vaccine strain, Alpha, Beta, and Gamma variants as well as T helper (Th)1 CD4 ⁺ -biased T cell responses. Although anti-receptor-binding domain (RBD)-specific antibody responses are initially predominant, the third immunization boosts significant non-RBD antibody titers. Challenging vaccinated animals with SARS-CoV-2 shows a complete protection through sterilizing immunity, which correlates with the presence of nasopharyngeal anti-S immunoglobulin G (IgG) and IgA titers. Thus, the S-LV approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing.

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Organizational Affiliation: 
• Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France.
Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France.
Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Location AMC, Amsterdam, the Netherlands.
Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France.
National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France.
Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 440.86 kDa 
• Atom Count: 23,694 
• Modeled Residue Count: 2,916 
• Deposited Residue Count: 3,864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 12		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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, P, Q, R	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 (Subject of Investigation/LOI)	AA [auth A], BA [auth A], CA [auth A], 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 B], MA [auth B], NA [auth B], OA [auth C], PA [auth C], QA [auth C], 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], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], 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: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): Sulbaran, G., Effantin, G., Schoehn, G., Weissenhorn, W.

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Funding Organization	Location	Grant Number
European Union (EU)	France	681032, H2020 EHVA
Agence Nationale de la Recherche (ANR)	France	RA-Covid-19

Revision History  

• Version 1.0: 2022-03-09
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2025-07-09
  Changes: Data collection