7EB3

Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 3

Summary for 7EB3

• Entry DOI: 10.2210/pdb7eb3/pdb
• Related: 7EAZ 7EB0
• EMDB information: 31047 31048 31050
• Descriptor: Spike glycoprotein, beta-D-mannopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: sars-cov-2, spike protein, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2)
• Total number of polymer chains: 3
• Total formula weight: 443410.81

Authors

Yang, T.J.,Yu, P.Y.,Chang, Y.C.,Hsu, S.T.D. (deposition date: 2021-03-08, release date: 2021-06-23, Last modification date: 2024-10-16)

Primary citation

Yang, T.J.,Yu, P.Y.,Chang, Y.C.,Hsu, S.D.
D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation.
J.Biol.Chem., 297:101238-101238, 2021

PubMed Abstract: The D614G mutation in the spike protein of SARS-CoV-2 alters the fitness of the virus, leading to the dominant form observed in the COVID-19 pandemic. However, the molecular basis of the mechanism by which this mutation enhances fitness is not clear. Here we demonstrated by cryo-electron microscopy that the D614G mutation resulted in increased propensity of multiple receptor-binding domains (RBDs) in an upward conformation poised for host receptor binding. Multiple substates within the one RBD-up or two RBD-up conformational space were determined. According to negative staining electron microscopy, differential scanning calorimetry, and differential scanning fluorimetry, the most significant impact of the mutation lies in its ability to eliminate the unusual cold-induced unfolding characteristics and to significantly increase the thermal stability under physiological pH. The D614G spike variant also exhibited exceptional long-term stability when stored at 37 °C for up to 2 months. Our findings shed light on how the D614G mutation enhances the infectivity of SARS-CoV-2 through a stabilizing mutation and suggest an approach for better design of spike protein-based conjugates for vaccine development.

PubMed: 34563540
DOI: 10.1016/j.jbc.2021.101238

Experimental method

ELECTRON MICROSCOPY (3.6 Å)