CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Nat Commun. 2022 Aug 24;13(1):4958. doi: 10.1038/s41467-022-32665-7.
Omicron SARS-CoV-2 is rapidly spreading worldwide. To delineate the impact of emerging mutations on spike's properties, we performed systematic structural analyses on apo Omicron spike and its complexes with human ACE2 or S309 neutralizing antibody (NAb) by cryo-EM. The Omicron spike preferentially adopts the one-RBD-up conformation both before and after ACE2 binding, which is in sharp contrast to the orchestrated conformational changes to create more up-RBDs upon ACE2 binding as observed in the prototype and other four variants of concern (VOCs). Furthermore, we found that S371L, S373P and S375F substitutions enhance the stability of the one-RBD-up conformation to prevent exposing more up-RBDs triggered by ACE2 binding. The increased stability of the one-RBD-up conformation restricts the accessibility of S304 NAb, which targets a cryptic epitope in the closed conformation, thus facilitating the immune evasion by Omicron. These results expand our understanding of Omicron spike's conformation, receptor binding and antibody evasion mechanism.
奥密克戎 SARS-CoV-2 正在全球迅速传播。为了阐明新出现的突变对刺突蛋白特性的影响,我们通过冷冻电镜对无配体奥密克戎刺突蛋白及其与人 ACE2 或 S309 中和抗体(NAb)的复合物进行了系统的结构分析。奥密克戎刺突蛋白在与 ACE2 结合前后优先采用一个 RBD 朝上的构象,这与在原型和其他四个关注变体(VOC)中观察到的 ACE2 结合后通过协调构象变化来产生更多朝上 RBD 的情况形成鲜明对比。此外,我们发现 S371L、S373P 和 S375F 取代增强了一个 RBD 朝上构象的稳定性,以防止 ACE2 结合触发更多朝上 RBD 的暴露。一个 RBD 朝上构象的稳定性增加限制了 S304 NAb 的可及性,S304 NAb 靶向封闭构象中的隐蔽表位,从而促进了奥密克戎的免疫逃逸。这些结果扩展了我们对奥密克戎刺突蛋白构象、受体结合和抗体逃逸机制的理解。