EMD-45866
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 1 open RBD
EMD-45866
Single-particle4.0 Å
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Map released: 27/11/2024
Last modified: 25/12/2024
Sample Organism:
Severe acute respiratory syndrome coronavirus 2
Sample: Severe acute respiratory syndrome coronavirus 2
Fitted models: 9crf (Avg. Q-score: 0.349)
Deposition Authors: Ke Z
,
Croll TI
,
Briggs JAG
Sample: Severe acute respiratory syndrome coronavirus 2
Fitted models: 9crf (Avg. Q-score: 0.349)
Deposition Authors: Ke Z
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Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Ke Z
,
Peacock TP
,
Brown JC
,
Sheppard CM
,
Croll TI
,
Kotecha A
,
Goldhill DH
,
Barclay WS
,
Briggs JAG
(2024) EMBO J , 43 , 6469 - 6495
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(2024) EMBO J , 43 , 6469 - 6495
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.
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.