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

Abstract

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.

Structural insights into coronavirus entry

“…Recent structural work comparing recombinant S proteins from SARS-CoV and MERS-CoV in isolation and in complex with their cognate receptors or neutralizing antibodies suggested an activation mechanism for coronavirus fusion (Gui et al, 2017;Kirchdoerfer et al, 2018; Song et al, 2018;Walls et al, 2019;Yuan et al, 2017). Specifically, SARS-CoV and MERS-CoV S structures in complex with neutralizing antibodies isolated from survivors showed both antibodies competitively blocked receptor interaction, in agreement with previous surface plasmon resonance data (Corti et al, 2015;Rockx et al, 2008;Traggiai et al, 2004;Walls et al, 2019).…”

“…Free 9-O-Ac-Sia, however, did not trigger S conformational changes associated with membrane fusion . This observation contrasts with data for SARS-CoV S, for which addition of the human angiotensin-converting enzyme 2 (ACE2) ectodomain (the proteinaceous receptor) promoted S refolding to the postfusion state (Song et al, 2018;Walls et al, 2019). These findings suggested that either 9-O-Ac-Sia-containing receptors differ from proteinaceous receptors in their mode of action, or that an interaction with a yet unidentified proteinaceous receptor is required before or after virus internalization for HCoV-OC43 entry into target cells.…”

“…Recent cryoEM studies revealed that MERS-CoV S and SARS-CoV S can adopt open and closed conformations in which the receptor binding site of domain B is exposed and occluded, respectively (Gui et al, 2017;Kirchdoerfer et al, 2018;Pallesen et al, 2017;Song et al, 2018;Walls et al, 2019;Yuan et al, 2017). In contrast, the MHV, HCoV-NL63, HCoV-HKU1, PDCoV, IBV and HCoV-OC43 S glycoproteins appear to only adopt a closed conformation (Kirchdoerfer et al, 2016;Shang et al, 2018a, b;Tortorici et al, 2019;Walls et al, 2016a, b;Xiong et al, 2018) and unknown trigger(s), besides proteolytic activation, might be necessary for these viruses to expose their receptor-binding motifs for recognition to occur.…”

“…4). These observations suggested that upon receptor recognition, bound B domains are locked in the open state, thereby releasing the constraints imposed on the HR1-central helix hairpin, allowing refolding of the S 2 fusion machinery and membrane fusion to occur (Pallesen et al, 2017;Song et al, 2018;Walls et al, 2019;Yuan et al, 2017) (Fig. 4).…”

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

“…Since binding of ACE2 to the isolated B domain was Figure S3 and Tables S4 and S5. reported to have an equilibrium dissociation constant (K D ) in the nanomolar range (Li et al, 2005c), one would expect that full saturation should occur rapidly in the conditions of our experiments (100-fold concentration excess over the K D ). Previous reports, however, suggested a lower affinity of the fulllength S trimer, relative to the isolated B domain, for ACE2 (Kirchdoerfer et al, 2018;Matsuyama and Taguchi, 2009;Song et al, 2018). We propose that the conformational landscape of the B domains in the context of the SARS-CoV S trimer, sampling open and closed conformations, decreases the apparent binding affinity for ACE2 and S230 due to masking of their binding sites in the closed state.…”