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Cryo-EM structure of SARS-CoV-2 BA.4/5 spike protein in complex with 1G11 (local refinement)Cryo-EM structure of SARS-CoV-2 BA.4/5 spike protein in complex with 1G11 (local refinement)
Structural highlights
FunctionSPIKE_SARS2 attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099][1] [2] [3] mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099] Publication Abstract from PubMedThe continuous emergence of SARS-CoV-2 variants, particularly the newly circulating Omicron XBB subvariants, has led to a significant reduction in the neutralizing potency and breadth of antibodies. In this study, we report a SARS-CoV-2 human neutralizing antibody, 1G11, which potently and broadly neutralizes diverse variants, including Omicron subvariants BA.4/5 and BF.7, but is evaded by the recently emerged BQ.1.1 and XBBs. Cryo-electron microscopy structure analysis of the 1G11 in complex with the BA.4/5 spike trimer reveals that 1G11, a Class 3 nAb, recognizes an epitope similar to those of S309 and LY-CoV1404. Structurally, the mutations K444T and V445P in BQ.1.1 and XBB subvariants are found to disrupt the interface between 1G11 and the spike protein, resulting in antibody evasion. 1G11 is further demonstrated to mediate neutralization through multiple mechanisms, including receptor binding blockage, interspike cross-linking, Fc-mediated ADCC and ADCP. Collectively, these findings provide insights into a better understanding of neutralizing antibody evasion and highlight the potential for broad neutralization by structure-based modification of available antibodies. IMPORTANCE The ongoing COVID-19 pandemic has been characterized by the emergence of new SARS-CoV-2 variants including the highly transmissible Omicron XBB sublineages, which have shown significant resistance to neutralizing antibodies (nAbs). This resistance has led to decreased vaccine effectiveness and therefore result in breakthrough infections and reinfections, which continuously threaten public health. To date, almost all available therapeutic nAbs, including those authorized under Emergency Use Authorization nAbs that were previously clinically useful against early strains, have recently been found to be ineffective against newly emerging variants. In this study, we provide a comprehensive structural basis about how the Class 3 nAbs, including 1G11 in this study and noted LY-CoV1404, are evaded by the newly emerged SARS-CoV-2 variants. Structural basis for broad neutralization of human antibody against Omicron sublineages and evasion by XBB variant.,Sun H, Wang Y, Chen X, Jiang Y, Wang S, Huang Y, Liu L, Li Y, Lan M, Guo H, Yuan Q, Zhang Y, Li T, Yu H, Gu Y, Zhang J, Li S, Zheng Z, Zheng Q, Xia N J Virol. 2023 Oct 19:e0113723. doi: 10.1128/jvi.01137-23. PMID:37855619[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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