7THK

Cryo-EM structure of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant

Summary for 7THK

• Entry DOI: 10.2210/pdb7thk/pdb
• EMDB information: 25896
• Descriptor: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose (2 entities in total)
• Functional Keywords: fusion protein, spike glycoprotein, covid-19, rbd, ntd, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 426815.81

Authors

Cerutti, G.,Shapiro, L. (deposition date: 2022-01-11, release date: 2022-03-02, Last modification date: 2024-11-06)

Primary citation

Cerutti, G.,Guo, Y.,Liu, L.,Liu, L.,Zhang, Z.,Luo, Y.,Huang, Y.,Wang, H.H.,Ho, D.D.,Sheng, Z.,Shapiro, L.
Cryo-EM structure of the SARS-CoV-2 Omicron spike.
Cell Rep, 38:110428-110428, 2022

PubMed Abstract: The recently reported B.1.1.529 Omicron variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) includes 34 mutations in the spike protein relative to the Wuhan strain, including 15 mutations in the receptor-binding domain (RBD). Functional studies have shown Omicron to substantially escape the activity of many SARS-CoV-2-neutralizing antibodies. Here, we report a 3.1 Å-resolution cryoelectron microscopy (cryo-EM) structure of the Omicron spike protein ectodomain. The structure depicts a spike that is exclusively in the 1-RBD-up conformation with high mobility of RBD. Many mutations cause steric clashes and/or altered interactions at antibody-binding surfaces, whereas others mediate changes of the spike structure in local regions to interfere with antibody recognition. Overall, the structure of the Omicron spike reveals how mutations alter its conformation and explains its extraordinary ability to evade neutralizing antibodies.

PubMed: 35172173
DOI: 10.1016/j.celrep.2022.110428

Experimental method

ELECTRON MICROSCOPY (3.11 Å)