8GB0

SARS-CoV-2 Spike H655Y variant, One RBD Open

Summary for 8GB0

• Entry DOI: 10.2210/pdb8gb0/pdb
• EMDB information: 29910
• Descriptor: Spike glycoprotein (1 entity in total)
• Functional Keywords: sars-cov-2, spike protein, glycoprotein, trimeric complex, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 3
• Total formula weight: 427500.66

Authors

Egri, S.B.,Shen, K.,Luban, J. (deposition date: 2023-02-24, release date: 2023-04-26, Last modification date: 2025-05-14)

Primary citation

Yurkovetskiy, L.,Egri, S.,Kurhade, C.,Diaz-Salinas, M.A.,Jaimes, J.A.,Nyalile, T.,Xie, X.,Choudhary, M.C.,Dauphin, A.,Li, J.Z.,Munro, J.B.,Shi, P.Y.,Shen, K.,Luban, J.
S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness.
Biorxiv, 2023

PubMed Abstract: SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.

PubMed: 37034621
DOI: 10.1101/2023.03.30.535005

Experimental method

ELECTRON MICROSCOPY (4.1 Å)