8DLO image
Entry Detail
PDB ID:
8DLO
EMDB ID:
Keywords:
Title:
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein
Biological Source:
PDB Version:
Deposition Date:
2022-07-08
Release Date:
2022-08-31
Method Details:
Experimental Method:
Resolution:
2.25 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Chain IDs:A, B, C
Chain Length:1288
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun 13 4696 4696 (2022)
PMID: 35982054 DOI: 10.1038/s41467-022-32262-8

Abstact

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 (VH 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.

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