Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1

Abstract

Human coronavirus (CoV) HKU1 is a pathogen causing acute respiratory illnesses and so far little is known about its biology. HKU1 virus uses its S1 subunit C-terminal domain (CTD) and not the N-terminal domain like other lineage A β-CoVs to bind to its yet unknown human receptor. Here we present the crystal structure of HKU1 CTD at 1.9 Å resolution. The structure consists of three subdomains: core, insertion and subdomain-1 (SD-1). While the structure of the core and SD-1 subdomains of HKU1 are highly similar to those of other β-CoVs, the insertion subdomain adopts a novel fold, which is largely invisible in the cryo-EM structure of the HKU1 S trimer. We identify five residues in the insertion subdomain that are critical for binding of neutralizing antibodies and two residues essential for receptor binding. Our study contributes to a better understanding of entry, immunity and evolution of CoV S proteins.

Human coronaviruses OC43 and HKU1 bind to 9- O -acetylated sialic acids via a conserved receptor-binding site in spike protein domain A

“…However, HKU1, like the β1CoVs, uses 9-O-Ac-sialoglycans for attachment and the binding to these receptors is essential for infection (14). According to recent publications, the RBS would not be in S1 A , but in a downstream domain (31,32), the main argument being that HKU1 S1 A does not detectably bind to glycoconjugates (30). Indeed, we also did not detect binding of HKU1 S1 A -Fc, at least not by standard sp-LBA and conventional HAA ( Fig.…”

“…To further study whether this site is involved in 9-O-Ac-Sia binding and to understand the structural basis for the considerable difference in affinity between HKU1 and β1CoV S1 A domains, we performed a side-by-side structure comparison. While in β1CoV S1 A domains the RBS is readily accessible, the corresponding site in HKU1 S1 A is located at the bottom of a canyon because it is flanked by protruding parallel ridges comprised of HKU1 S1 A residues 28 through 34 [element (e)1 corresponding to BCoV L2β2 residues [29][30][31][32][33][34][35], and 243 through 252 (e2 corresponding to BCoV residues 253-256 in the β18-β19 loop), each decorated with an N-linked glycan ( Fig. 6B; see also SI Appendix, Fig.…”

“…Although this model remains to be confirmed, it has been widely accepted by the field (27,28,(31)(32)(33). Surprisingly, HKU1 S was recently reported to bind to its receptor via a domain other than S1 A (31). Despite the similarity of HKU1 domain A to that of BCoV and OC43, binding of HKU1 S1 A to 9-O-Ac-Sia was reportedly not detectable (30,31).…”

“…Based on the galectin-like fold of the S1 A domain and mutational analysis, the RBS was predicted (17). Although this model remains to be confirmed, it has been widely accepted by the field (27,28,(31)(32)(33). Surprisingly, HKU1 S was recently reported to bind to its receptor via a domain other than S1 A (31).…”

“…Surprisingly, HKU1 S was recently reported to bind to its receptor via a domain other than S1 A (31). Despite the similarity of HKU1 domain A to that of BCoV and OC43, binding of HKU1 S1 A to 9-O-Ac-Sia was reportedly not detectable (30,31). Prompted by these observations and the fact that the predicted RBS in β1CoV S1 A in its design and architecture bears no resemblance to other 9-O-Ac-Sia binding sites, we sought to test the published model.…”