Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution

Nat Commun. 2021 Mar 11;12(1):1607. doi: 10.1038/s41467-021-21767-3.

Abstract

In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the "down" conformation, indicating they are more prone to adopt the receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. We further identified critical residues in the RBD underlying different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes. These results collectively indicate that tight RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Angiotensin-Converting Enzyme 2 / chemistry
  • Animals
  • COVID-19 / epidemiology
  • COVID-19 / transmission
  • COVID-19 / virology*
  • Chiroptera / virology*
  • Coronavirus / chemistry*
  • Coronavirus / genetics*
  • Cryoelectron Microscopy
  • Evolution, Molecular
  • Host Microbial Interactions
  • Humans
  • Models, Molecular
  • Pandemics
  • Pangolins / virology*
  • Protein Domains
  • SARS-CoV-2 / chemistry*
  • SARS-CoV-2 / genetics*
  • Sequence Homology, Amino Acid
  • Species Specificity
  • Spike Glycoprotein, Coronavirus / chemistry*
  • Spike Glycoprotein, Coronavirus / genetics*
  • Spike Glycoprotein, Coronavirus / ultrastructure

Substances

  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2