9CRG

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed RBDs

Summary for 9CRG

• Entry DOI: 10.2210/pdb9crg/pdb
• Related: 9CRC 9CRD 9CRE 9CRF
• EMDB information: 45863 45864 45865 45866 45867
• 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-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: sars-cov-2 variant, gamma (p.1) variant, virus
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 441233.74

Authors

Ke, Z.,Kotecha, A.,Briggs, J.A.G. (deposition date: 2024-07-22, release date: 2024-11-27, Last modification date: 2024-12-25)

Primary citation

Ke, Z.,Peacock, T.P.,Brown, J.C.,Sheppard, C.M.,Croll, T.I.,Kotecha, A.,Goldhill, D.H.,Barclay, W.S.,Briggs, J.A.G.
Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43:6469-6495, 2024

PubMed Abstract: 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.

PubMed: 39543395
DOI: 10.1038/s44318-024-00303-1

Experimental method

ELECTRON MICROSCOPY (3.3 Å)