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Structure paper

TitleCryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 1214, Year 2022
Publish dateMar 3, 2022
AuthorsGang Ye / Bin Liu / Fang Li /
PubMed AbstractThe omicron variant of SARS-CoV-2 has been spreading rapidly across the globe. The virus-surface spike protein plays a critical role in the cell entry and immune evasion of SARS-CoV-2. Here we ...The omicron variant of SARS-CoV-2 has been spreading rapidly across the globe. The virus-surface spike protein plays a critical role in the cell entry and immune evasion of SARS-CoV-2. Here we determined the 3.0 Å cryo-EM structure of the omicron spike protein ectodomain. In contrast to the original strain of SARS-CoV-2 where the receptor-binding domain (RBD) of the spike protein takes a mixture of open ("standing up") and closed ("lying down") conformations, the omicron spike molecules are predominantly in the open conformation, with one upright RBD ready for receptor binding. The open conformation of the omicron spike is stabilized by enhanced inter-domain and inter-subunit packing, which involves new mutations in the omicron strain. Moreover, the omicron spike has undergone extensive mutations in RBD regions where known neutralizing antibodies target, allowing the omicron variant to escape immune surveillance aimed at the original viral strain. The stable open conformation of the omicron spike sheds light on the cell entry and immune evasion mechanisms of the omicron variant.
External linksNat Commun / PubMed:35241675 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.2 Å
Structure data

25887

7tgw

EMDB-25887, PDB-7tgw:
Omicron spike at 3.0 A (open form)
Method: EM (single particle) / Resolution: 3.0 Å

25888

7tgx

EMDB-25888, PDB-7tgx:
Prototypic SARS-CoV-2 G614 spike (open form)
Method: EM (single particle) / Resolution: 3.2 Å

25889

7tgy

EMDB-25889, PDB-7tgy:
Prototypic SARS-CoV-2 G614 spike (closed form)
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-MAN:
alpha-D-mannopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SARS-CoV-2 / omicron spike / Prototypic SARS-CoV-2 G614 spike

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