9ELI

Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (closed state)

9ELI の概要

• エントリーDOI: 10.2210/pdb9eli/pdb
• EMDBエントリー: 48150
• 分子名称: Spike glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• 機能のキーワード: sars-cov-2, covid-19, spike, 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: 411524.28

構造登録者

Feng, Z.,Huang, J.,Ward, A.B. (登録日: 2024-12-04, 公開日: 2025-05-28, 最終更新日: 2025-07-16)

主引用文献

Feng, Z.,Huang, J.,Baboo, S.,Diedrich, J.K.,Bangaru, S.,Paulson, J.C.,Yates 3rd, J.R.,Yuan, M.,Wilson, I.A.,Ward, A.B.
Structural and functional insights into the evolution of SARS-CoV-2 KP.3.1.1 spike protein.
Cell Rep, 44:115941-115941, 2025

PubMed Abstract: The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigate how mutations and a deletion in the KP.3.1.1 spike protein (S) affect hACE2 binding and antibody escape. Mass spectrometry confirms a new glycan site at residue N30 that alters the glycoforms at neighboring N61. Cryoelectron microscopy (cryo-EM) structures show that the N30 glycan and rearrangement of adjacent residues do not significantly change the overall spike structure, up-down ratio of receptor-binding domains (RBDs), or hACE2 binding. Furthermore, a KP.3.1.1 S with hACE2 structure further confirms an epistatic effect between F456L and Q493E on hACE2 binding. Our analysis shows that SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.

PubMed: 40618371
DOI: 10.1016/j.celrep.2025.115941

実験手法

ELECTRON MICROSCOPY (2.82 Å)