Research Article: Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2

Date Published: August 13, 2018

Publisher: Public Library of Science

Author(s): Wenfei Song, Miao Gui, Xinquan Wang, Ye Xiang, Mark T. Heise.


The trimeric SARS coronavirus (SARS-CoV) surface spike (S) glycoprotein consisting of three S1-S2 heterodimers binds the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediates fusion of the viral and cellular membranes through a pre- to postfusion conformation transition. Here, we report the structure of the SARS-CoV S glycoprotein in complex with its host cell receptor ACE2 revealed by cryo-electron microscopy (cryo-EM). The complex structure shows that only one receptor-binding domain of the trimeric S glycoprotein binds ACE2 and adopts a protruding “up” conformation. In addition, we studied the structures of the SARS-CoV S glycoprotein and its complexes with ACE2 in different in vitro conditions, which may mimic different conformational states of the S glycoprotein during virus entry. Disassociation of the S1-ACE2 complex from some of the prefusion spikes was observed and characterized. We also characterized the rosette-like structures of the clustered SARS-CoV S2 trimers in the postfusion state observed on electron micrographs. Structural comparisons suggested that the SARS-CoV S glycoprotein retains a prefusion architecture after trypsin cleavage into the S1 and S2 subunits and acidic pH treatment. However, binding to the receptor opens up the receptor-binding domain of S1, which could promote the release of the S1-ACE2 complex and S1 monomers from the prefusion spike and trigger the pre- to postfusion conformational transition.

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Coronaviruses are a family of large, enveloped, positive-stranded RNA viruses that cause upper respiratory, gastrointestinal and central nervous system diseases in humans and other animals [1]. Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 circulate in humans and cause mild respiratory diseases [2]. However, the outbreak of SARS-CoV in 2002 and MERS-CoV in 2012 showed that coronaviruses can cross the species barrier and emerge as highly pathogenic viruses [3]. The high fatality rate and wide spread of these new emerging coronaviruses indicate that they are a severe threat to global health.

Proteolysis is key to coronavirus entry. Unlike the S glycoproteins of MERS-CoV and MHV, the SARS-CoV S glycoprotein is not cleaved at the S1/S2 site during virus packaging in cells and, hence, remains uncleaved on mature virions [22, 23]. However, cleavage of the precursor S protein at the S1/S2 cleavage site by extracellular or endosome proteases is required for a functional SARS-CoV S glycoprotein [24]. Previous studies showed that blockage of the pH decrease in endosomes slightly reduced SARS-CoV infection, which indicated that low pH is not an essential factor for virus entry [25, 26]. Here, our results showed that the prefusion architecture, either in the unbound or ACE2-bound state, was retained in the cleaved S glycoprotein, and the conformational heterogeneity of CTD1s still existed. Similar results were also obtained for the cleaved with/without low-pH treatment S glycoproteins. Therefore, although cleavage at the S1/S2 site is required for a functional S glycoprotein, it does not significantly affect the overall architecture and conformation heterogeneity. However, we did observe significant differences between the mutant and wild-type cleaved S glycoproteins in binding ACE2, indicating that the S1/S2 cleavage site might affect CTD1 receptor binding, although the mechanism is still under investigation.