8V0S

SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.5)

8V0S の概要

• エントリーDOI: 10.2210/pdb8v0s/pdb
• EMDBエントリー: 42868
• 分子名称: Spike glycoprotein, 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: sars-cov-2, glycoprotein, trimer, viral protein
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 434774.20

構造登録者

Zhang, Q.E.,Acharya, P. (登録日: 2023-11-17, 公開日: 2024-06-12, 最終更新日: 2024-11-06)

主引用文献

Zhang, Q.E.,Lindenberger, J.,Parsons, R.J.,Thakur, B.,Parks, R.,Park, C.S.,Huang, X.,Sammour, S.,Janowska, K.,Spence, T.N.,Edwards, R.J.,Martin, M.,Williams, W.B.,Gobeil, S.,Montefiori, D.C.,Korber, B.,Saunders, K.O.,Haynes, B.F.,Henderson, R.,Acharya, P.
SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition.
Mol.Cell, 84:2747-2764.e7, 2024

PubMed Abstract: A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.

PubMed: 39059371
DOI: 10.1016/j.molcel.2024.06.028

実験手法

ELECTRON MICROSCOPY (3.3 Å)