8DLL

Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein

Summary for 8DLL

• Entry DOI: 10.2210/pdb8dll/pdb
• EMDB information: 27505
• 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, glycoprotein, fusion protein, viral protein, beta, b.1.351
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 439906.57

Authors

Zhu, X.,Mannar, D.,Saville, J.W.,Srivastava, S.S.,Berezuk, A.M.,Zhou, S.,Tuttle, K.S.,Subramaniam, S. (deposition date: 2022-07-08, release date: 2022-08-31, Last modification date: 2024-11-20)

Primary citation

Mannar, D.,Saville, J.W.,Sun, Z.,Zhu, X.,Marti, M.M.,Srivastava, S.S.,Berezuk, A.M.,Zhou, S.,Tuttle, K.S.,Sobolewski, M.D.,Kim, A.,Treat, B.R.,Da Silva Castanha, P.M.,Jacobs, J.L.,Barratt-Boyes, S.M.,Mellors, J.W.,Dimitrov, D.S.,Li, W.,Subramaniam, S.
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13:4696-4696, 2022

PubMed Abstract: Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (V ab6) that neutralizes all major variants including the recently emerged BA.1 and BA.2 Omicron subvariants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within previously emerged variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.

PubMed: 35982054
DOI: 10.1038/s41467-022-32262-8

Experimental method

ELECTRON MICROSCOPY (2.56 Å)