9F9Y

SARS-CoV-2 BA-2.87.1 Spike ectodomain

Summary for 9F9Y

• Entry DOI: 10.2210/pdb9f9y/pdb
• EMDB information: 50263
• Descriptor: Spike glycoprotein,Fibritin, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: viral protein, immune system, sars-cov-2, rbd, spike, glycoprotein, ba.2.87.1, receptor, coronavirus-2, n-terminal domain, supersite
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 3
• Total formula weight: 430954.17

Authors

Ren, J.,Stuart, D.I.,Duyvesteyn, H.M.E. (deposition date: 2024-05-09, release date: 2024-08-21, Last modification date: 2024-10-16)

Primary citation

Duyvesteyn, H.M.E.,Dijokaite-Guraliuc, A.,Liu, C.,Supasa, P.,Kronsteiner, B.,Jeffery, K.,Stafford, L.,Klenerman, P.,Dunachie, S.J.,Mongkolsapaya, J.,Fry, E.E.,Ren, J.,Stuart, D.I.,Screaton, G.R.
Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike.
Structure, 32:1594-, 2024

PubMed Abstract: BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an "all-down" conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.

PubMed: 39173622
DOI: 10.1016/j.str.2024.07.020

Experimental method

ELECTRON MICROSCOPY (2.8 Å)