9AYX

SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)

Summary for 9AYX

• Entry DOI: 10.2210/pdb9ayx/pdb
• EMDB information: 44001
• Descriptor: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose (2 entities in total)
• Functional Keywords: sars-cov-2, glycoprotein, trimer, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 433261.88

Authors

Zhang, Q.E.,Acharya, P. (deposition date: 2024-03-08, release date: 2024-06-12, Last modification date: 2024-11-06)

Primary citation

Zhang, Q.E.,Lindenberger, J.,Parsons, R.J.,Thakur, B.,Parks, R.,Park, C.S.,Huang, X.,Sammour, S.,Janowska, K.,Spence, T.N.,Edwards, R.J.,Martin, M.,Williams, W.B.,Gobeil, S.,Montefiori, D.C.,Korber, B.,Saunders, K.O.,Haynes, B.F.,Henderson, R.,Acharya, P.
SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition.
Mol.Cell, 84:2747-2764.e7, 2024

PubMed Abstract: A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.

PubMed: 39059371
DOI: 10.1016/j.molcel.2024.06.028

Experimental method

ELECTRON MICROSCOPY (3 Å)