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

Long Tian,Xinquan Wang,Jinfang Yu,Shuyuan Zhang,Sisi Shan,Jun Lan,Linqi Zhang,Shuyuan Qiao,Jianwei Zeng

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.

Highlights

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
Coronaviruses RaTG13 isolated from bat and PCoV_GX isolated from pangolin are closely related to the SARSCoV-2
The residues Y449, Q493, Q498, N501, and Y505 cluster together to form a patch on the SARS-CoV-2 receptor-binding domains (RBDs) that has significant hydrophilic interactions with human ACE2 (hACE2)

Summary

Introduction

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. 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. Coronavirus RaTG13, detected in the horseshoe bat Rhinolophus affinis in China’s Yunnan province, was identified as the closest relative of the SARS-CoV-25 It shares 96.2% sequence identity with the SARSCoV-2 genome, reflecting the likely origin of SARS-CoV-2 in bats[5]. The comparisons of the RaTG13, PCoV_GX, and SARSCoV-2 spike structures, the strength of their binding with hACE2, and their efficiency in facilitating pseudovirus cell entry provide important insights into the evolution and cross-species transmission of SARS-CoV-2

Methods

Results

Conclusion