Receptor-binding loops in alphacoronavirus adaptation and evolution

Abstract

RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding.

Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus

“…Purified pAPN ectodomain was crystallized with one molecule in each asymmetric unit and its crystal structure was determined at 2.65 Å in a C121 space group (Table 3). As described previously [22,24,43,63,64], pAPN ectodomain adopts a hook-like conformation or so-called seahorse shape ( Fig. 5B and C).…”

“…7B). In contrast, HCoV-229E [22] and TGEV [24] RBDs had high affinities to their receptor APN. These results were similar to SARS-CoV RBD not binding to DPP4 or MERS-CoV RBD not binding to ACE2, while the K D of DPP4 binding to MERS-CoV RBD was about 16.7 nM (K on : 1.79 × 10 5 M −1 s −1 , K off : 2.99 × 10 −3 M −1 s −1 ) [20].…”

“…In the current study, three canonical assays were carried out to characterize the interaction between pAPN ectodomain and PEDV S1 or S1t protein since these functional target proteins were successfully prepared. According to previous reports, coronavirus S-RBDs and their host receptors have high affinities and yield stable complexes in vitro, which can be obtained by gel filtration chromatography [17,20,22,24,69,70]. Therefore, we firstly characterized the interaction between pAPN ectodomain and PEDV S1 or S1t protein by gel filtration chromatography.…”

“…The viral receptor-binding domains (RBD) are located in the C-terminal domains (CTDs) of the S1 subunits (S1-CTDs) [17,19,20]. Human coronavirus 229E (HCoV-229E) [21,22] and TGEV [23,24] utilize aminopeptidase N (APN) as the host receptor and their RBDs are also located in the S1-CTDs [22,24].…”

Structural insights into coronavirus entry

“…Although several class 1 viral fusion proteins have been extensively studied, CoV S proteins have proven reluctant to structural characterization until recently. Structural studies were largely limited to X-ray crystallographic analysis of isolated receptor-binding domains in complex with viral receptor ectodomains or neutralizing antibodies (Li et al, 2005a;Lu et al, 2013;Peng et al, 2011;Prabakaran et al, 2006;Reguera et al, 2012;Wang et al, 2013;Wong et al, 2017;Wu et al, 2009;Yu et al, 2015) and of the S 2 postfusion core (Duquerroy et al, 2005;Gao et al, 2013;Supekar et al, 2004;Xu et al, 2004a, b;Zheng et al, 2006) with the exception of two low-resolution electron microscopy reports (Beniac et al, 2006(Beniac et al, , 2007. In the past few years, however, technical advances in single-particle cryo-electron microscopy (cryoEM) (Bai et al, 2013;Brilot et al, 2012;Campbell et al, 2012Campbell et al, , 2015Li et al, 2013;Punjani et al, 2017;Scheres, 2012) together with the implementation of strategies for the stabilization of CoV S proteins in prefusion conformation (Pallesen et al, 2017;Walls et al, 2017a) led to a surge of structural data for multiple S ectodomain trimers.…”