7TGW

Omicron spike at 3.0 A (open form)

Summary for 7TGW

• Entry DOI: 10.2210/pdb7tgw/pdb
• EMDB information: 25887 25888 25889
• Descriptor: 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)
• Functional Keywords: sars-cov-2, omicron spike, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 421354.35

Authors

Ye, G.,Liu, B.,Li, F. (deposition date: 2022-01-09, release date: 2022-03-09, Last modification date: 2024-11-20)

Primary citation

Ye, G.,Liu, B.,Li, F.
Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain.
Nat Commun, 13:1214-1214, 2022

PubMed Abstract: The omicron variant of SARS-CoV-2 has been spreading rapidly across the globe. The virus-surface spike protein plays a critical role in the cell entry and immune evasion of SARS-CoV-2. Here we determined the 3.0 Å cryo-EM structure of the omicron spike protein ectodomain. In contrast to the original strain of SARS-CoV-2 where the receptor-binding domain (RBD) of the spike protein takes a mixture of open ("standing up") and closed ("lying down") conformations, the omicron spike molecules are predominantly in the open conformation, with one upright RBD ready for receptor binding. The open conformation of the omicron spike is stabilized by enhanced inter-domain and inter-subunit packing, which involves new mutations in the omicron strain. Moreover, the omicron spike has undergone extensive mutations in RBD regions where known neutralizing antibodies target, allowing the omicron variant to escape immune surveillance aimed at the original viral strain. The stable open conformation of the omicron spike sheds light on the cell entry and immune evasion mechanisms of the omicron variant.

PubMed: 35241675
DOI: 10.1038/s41467-022-28882-9

Experimental method

ELECTRON MICROSCOPY (3 Å)