8R87

Cryo-EM structure of the Sars-Cov2 S trimer without RBDs

Summary for 8R87

• Entry DOI: 10.2210/pdb8r87/pdb
• EMDB information: 18997
• Descriptor: Spike glycoprotein,Fibritin (1 entity in total)
• Functional Keywords: glycoprotein, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus; More
• Total number of polymer chains: 3
• Total formula weight: 350415.28

Authors

Effantin, G. (deposition date: 2023-11-28, release date: 2024-12-11, Last modification date: 2025-07-02)

Primary citation

Letscher, H.,Guilligay, D.,Effantin, G.,Amen, A.,Sulbaran, G.,Burger, J.A.,Bossevot, L.,Junges, L.,Leonec, M.,Morin, J.,Van Tilbeurgh, M.,Herate, C.,Gallouet, A.S.,Relouzat, F.,van der Werf, S.,Cavarelli, M.,Dereuddre-Bosquet, N.,van Gils, M.J.,Sanders, R.W.,Poignard, P.,Le Grand, R.,Weissenhorn, W.
RBD-depleted SARS-CoV-2 spike generates protective immunity in cynomolgus macaques.
Npj Vaccines, 10:63-63, 2025

PubMed Abstract: The SARS-CoV-2 pandemic revealed the rapid evolution of circulating strains. This led to new variants carrying mostly mutations within the receptor binding domain, which is immunodominant upon immunization and infection. In order to steer the immune response away from RBD epitopes to more conserved domains, we generated S glycoprotein trimers without RBD and stabilized them by formaldehyde cross-linking. The cryoEM structure demonstrated that SΔRBD folds into the native prefusion conformation, stabilized by one specific cross-link between S2 protomers. SΔRBD was coated onto lipid vesicles, to produce synthetic virus-like particles, SΔRBD-LV, which were utilized in a heterologous prime-boost strategy. Immunization of cynomolgus macaques either three times with the mRNA Comirnaty vaccine or two times followed by SΔRBD-LV showed that the SΔRBD-LV boost induced similar antibody titers and neutralization of different variants, including omicron. Upon challenge with omicron XBB.3, both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes conferred similar overall protection from infection for both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes. However, the SΔRBD-LV boost indicated better protection against lung infection than the Comirnaty strategy alone. Together our findings indicate that SΔRBD is highly immunogenic and provides improved protection compared to a third mRNA boost indicative of superior antibody-based protection.

PubMed: 40159504
DOI: 10.1038/s41541-025-01113-0

Experimental method

ELECTRON MICROSCOPY (3 Å)