Cryo-EM structure of coronavirus-HKU1 haemagglutinin esterase reveals architectural changes arising from prolonged circulation in humans

Daniel L Hurdiss,Joost Snijder,Ieva Drulyte,Yifei Lang,Raoul J De Groot,Tatiana M Shamorkina,Matti F Pronker,Frank J M Van Kuppeveld

doi:10.1038/s41467-020-18440-6

Daniel L Hurdiss, Joost Snijder + Show 6 more

Open Access

https://doi.org/10.1038/s41467-020-18440-6

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Abstract

The human betacoronaviruses HKU1 and OC43 (subgenus Embecovirus) arose from separate zoonotic introductions, OC43 relatively recently and HKU1 apparently much longer ago. Embecovirus particles contain two surface projections called spike (S) and haemagglutinin-esterase (HE), with S mediating receptor binding and membrane fusion, and HE acting as a receptor-destroying enzyme. Together, they promote dynamic virion attachment to glycan-based receptors, specifically 9-O-acetylated sialic acid. Here we present the cryo-EM structure of the ~80 kDa, heavily glycosylated HKU1 HE at 3.4 Å resolution. Comparison with existing HE structures reveals a drastically truncated lectin domain, incompatible with sialic acid binding, but with the structure and function of the esterase domain left intact. Cryo-EM and mass spectrometry analysis reveals a putative glycan shield on the now redundant lectin domain. The findings further our insight into the evolution and host adaptation of human embecoviruses, and demonstrate the utility of cryo-EM for studying small, heavily glycosylated proteins.

Highlights

The human betacoronaviruses HKU1 and OC43 arose from separate zoonotic introductions, OC43 relatively recently and HKU1 apparently much longer ago
The HKU1-A HE ectodomain was expressed as an Fc fusion protein in HEK293T cells and purified by protein A affinity chromatography, followed by on-the-bead thrombin cleavage to remove the Fc domain, and size exclusion chromatography (Supplementary Fig. 2A and Supplementary Table 2)
Single-particle analysis produced 2D class averages corresponding to different views of the HKU1 HE dimer (Fig. 1b)

Summary

Introduction

The human betacoronaviruses HKU1 and OC43 (subgenus Embecovirus) arose from separate zoonotic introductions, OC43 relatively recently and HKU1 apparently much longer ago. Human CoVs HKU1 and OC43 (subgenus Embecovirus, genus Betacoronavirus) are related but distinct[8] In immunocompetent individuals, these viruses are generally associated with common colds, but may cause significant morbidity and even mortality in the frail[9,10]. These viruses are generally associated with common colds, but may cause significant morbidity and even mortality in the frail[9,10] They entered the human population separately: HKU1 presumably several hundred years ago from a yet unknown animal reservoir[11,12], whereas OC43 entered far more recently (70–120 years ago), apparently from a bovine coronavirus (BCoV) spill-over[13]. A second type of envelope protein unique to embecoviruses, called the haemagglutinin-esterase (HE), serves as a receptor-destroying enzyme[8,16]

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