7TP8

Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D12 state

Summary for 7TP8

• Entry DOI: 10.2210/pdb7tp8/pdb
• EMDB information: 26048
• 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 spike protein trimer, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 439346.87

Authors

Gobeil, S.,Acharya, P. (deposition date: 2022-01-25, release date: 2022-02-09, Last modification date: 2024-10-23)

Primary citation

Gobeil, S.M.,Henderson, R.,Stalls, V.,Janowska, K.,Huang, X.,May, A.,Speakman, M.,Beaudoin, E.,Manne, K.,Li, D.,Parks, R.,Barr, M.,Deyton, M.,Martin, M.,Mansouri, K.,Edwards, R.J.,Eaton, A.,Montefiori, D.C.,Sempowski, G.D.,Saunders, K.O.,Wiehe, K.,Williams, W.,Korber, B.,Haynes, B.F.,Acharya, P.
Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82:2050-2068.e6, 2022

PubMed Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.

PubMed: 35447081
DOI: 10.1016/j.molcel.2022.03.028

Experimental method

ELECTRON MICROSCOPY (3.4 Å)