9F9Y

SARS-CoV-2 BA-2.87.1 Spike ectodomain

9F9Y の概要

• エントリーDOI: 10.2210/pdb9f9y/pdb
• EMDBエントリー: 50263
• 分子名称: 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)
• 機能のキーワード: viral protein, immune system, sars-cov-2, rbd, spike, glycoprotein, ba.2.87.1, receptor, coronavirus-2, n-terminal domain, supersite
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 430954.17

構造登録者

Ren, J.,Stuart, D.I.,Duyvesteyn, H.M.E. (登録日: 2024-05-09, 公開日: 2024-08-21, 最終更新日: 2024-10-16)

主引用文献

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

実験手法

ELECTRON MICROSCOPY (2.8 Å)