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TitleVirion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Journal, issue, pagesEMBO J, Year 2024
Publish dateNov 14, 2024
AuthorsZunlong Ke / Thomas P Peacock / Jonathan C Brown / Carol M Sheppard / Tristan I Croll / Abhay Kotecha / Daniel H Goldhill / Wendy S Barclay / John A G Briggs /
PubMed AbstractThe evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins, which are the major target for the adaptive immune response. Single- ...The evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins, which are the major target for the adaptive immune response. Single-particle cryo-EM analysis of soluble S protein from SARS-CoV-2 variants has revealed this structural adaptation at high resolution. The analysis of S trimers in situ on intact virions has the potential to provide more functionally relevant insights into S structure and virion morphology. Here, we characterized B.1, Alpha, Beta, Gamma, Delta, Kappa, and Mu variants by cryo-electron microscopy and tomography, assessing S cleavage, virion morphology, S incorporation, "in-situ" high-resolution S structures, and the range of S conformational states. We found no evidence for adaptive changes in virion morphology, but describe multiple different positions in the S protein where amino acid changes alter local protein structure. Taken together, our data are consistent with a model where amino acid changes at multiple positions from the top to the base of the spike cause structural changes that can modulate the conformational dynamics of the S protein.
External linksEMBO J / PubMed:39543395
MethodsEM (single particle)
Resolution2.8 - 4.0 Å
Structure data

45863

9crc

EMDB-45863, PDB-9crc:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 3 closed RBDs
Method: EM (single particle) / Resolution: 2.9 Å

45864

9crd

EMDB-45864, PDB-9crd:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 1 open RBD
Method: EM (single particle) / Resolution: 3.5 Å

45865

9cre

EMDB-45865, PDB-9cre:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 3 closed RBDs
Method: EM (single particle) / Resolution: 3.2 Å

45866

9crf

EMDB-45866, PDB-9crf:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 1 open RBD
Method: EM (single particle) / Resolution: 4.0 Å

45867

9crg

EMDB-45867, PDB-9crg:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed RBDs
Method: EM (single particle) / Resolution: 3.3 Å

45868

9crh

EMDB-45868, PDB-9crh:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs
Method: EM (single particle) / Resolution: 3.4 Å

45869

9cri

EMDB-45869, PDB-9cri:
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed RBDs
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

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

ChemComp-ZN:
Unknown entry

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SARS-CoV-2 variant / B.1 strain / Alpha (B.1.1.7) variant / VIRUS / Gamma (P.1) variant / Delta (B.1.617.2) variant / Mu (B.1.621) variant

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