8EPN

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation

Summary for 8EPN

• Entry DOI: 10.2210/pdb8epn/pdb
• EMDB information: 28531
• Descriptor: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: glycoprotein, trimer, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 396359.46

Authors

Williams, J.A.,Harshbarger, W. (deposition date: 2022-10-06, release date: 2023-06-21, Last modification date: 2024-11-20)

Primary citation

Williams, J.A.,Biancucci, M.,Lessen, L.,Tian, S.,Balsaraf, A.,Chen, L.,Chesterman, C.,Maruggi, G.,Vandepaer, S.,Huang, Y.,Mallett, C.P.,Steff, A.M.,Bottomley, M.J.,Malito, E.,Wahome, N.,Harshbarger, W.D.
Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity.
Sci Adv, 9:eadg0330-eadg0330, 2023

PubMed Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern challenge the efficacy of approved vaccines, emphasizing the need for updated spike antigens. Here, we use an evolutionary-based design aimed at boosting protein expression levels of S-2P and improving immunogenic outcomes in mice. Thirty-six prototype antigens were generated in silico and 15 were produced for biochemical analysis. S2D14, which contains 20 computationally designed mutations within the S2 domain and a rationally engineered D614G mutation in the SD2 domain, has an ~11-fold increase in protein yield and retains RBD antigenicity. Cryo-electron microscopy structures reveal a mixture of populations in various RBD conformational states. Vaccination of mice with adjuvanted S2D14 elicited higher cross-neutralizing antibody titers than adjuvanted S-2P against the SARS-CoV-2 Wuhan strain and four variants of concern. S2D14 may be a useful scaffold or tool for the design of future coronavirus vaccines, and the approaches used for the design of S2D14 may be broadly applicable to streamline vaccine discovery.

PubMed: 37285422
DOI: 10.1126/sciadv.adg0330

Experimental method

ELECTRON MICROSCOPY (2.8 Å)