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

2019 ◽  
Vol 116 (7) ◽  
pp. 2681-2690 ◽  
Author(s):  
Ruben J. G. Hulswit ◽  
Yifei Lang ◽  
Mark J. G. Bakkers ◽  
Wentao Li ◽  
Zeshi Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Receptor Binding ◽  
Protein S ◽  
Protein Domain ◽  
Spike Protein ◽  
Ligand Docking ◽  
Respiratory Pathogens ◽  
Receptor Binding Site ◽  
Human Coronaviruses

Human betacoronaviruses OC43 and HKU1 are endemic respiratory pathogens and, while related, originated from independent zoonotic introductions. OC43 is in fact a host-range variant of the species Betacoronavirus-1, and more closely related to bovine coronavirus (BCoV)—its presumptive ancestor—and porcine hemagglutinating encephalomyelitis virus (PHEV). The β1-coronaviruses (β1CoVs) and HKU1 employ glycan-based receptors carrying 9-O-acetylated sialic acid (9-O-Ac-Sia). Receptor binding is mediated by spike protein S, the main determinant of coronavirus host specificity. For BCoV, a crystal structure for the receptor-binding domain S1A is available and for HKU1 a cryoelectron microscopy structure of the complete S ectodomain. However, the location of the receptor-binding site (RBS), arguably the single-most important piece of information, is unknown. Here we solved the 3.0-Å crystal structure of PHEV S1A. We then took a comparative structural analysis approach to map the β1CoV S RBS, using the general design of 9-O-Ac-Sia-binding sites as blueprint, backed-up by automated ligand docking, structure-guided mutagenesis of OC43, BCoV, and PHEV S1A, and infectivity assays with BCoV-S–pseudotyped vesicular stomatitis viruses. The RBS is not exclusive to OC43 and related animal viruses, but is apparently conserved and functional also in HKU1 S1A. The binding affinity of the HKU1 S RBS toward short sialoglycans is significantly lower than that of OC43, which we attribute to differences in local architecture and accessibility, and which may be indicative for differences between the two viruses in receptor fine-specificity. Our findings challenge reports that would map the OC43 RBS elsewhere in S1A and that of HKU1 in domain S1B.

scholarly journals SARS-CoV-2 spike protein arrested in the closed state induces potent neutralizing responses

2021 ◽  
Author(s):  
George W. Carnell ◽  
Katarzyna A. Ciazynska ◽  
David A. Wells ◽  
Xiaoli Xiong ◽  
Ernest T. Aguinam ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Neutralizing Antibody ◽  
Protein S ◽  
Spike Protein ◽  
Receptor Binding Site ◽  
S Protein ◽  
Closed State ◽  
S Proteins ◽  
Protein Constructs

AbstractThe majority of SARS-CoV-2 vaccines in use or in advanced clinical development are based on the viral spike protein (S) as their immunogen. S is present on virions as pre-fusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described that act against both open and closed conformations. The long-term success of vaccination strategies will depend upon inducing antibodies that provide long-lasting broad immunity against evolving, circulating SARS-CoV-2 strains, while avoiding the risk of antibody dependent enhancement as observed with other Coronavirus vaccines. Here we have assessed the results of immunization in a mouse model using an S protein trimer that is arrested in the closed state to prevent exposure of the receptor binding site and therefore interaction with the receptor. We compared this with a range of other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induce a long-lived, strongly neutralizing antibody response as well as T-cell responses. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralising responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, virus-inhibiting immune responses than open spikes, and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. Together with their improved stability and storage properties we suggest that closed spikes may be a valuable component of refined, next-generation vaccines.

scholarly journals Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

2020 ◽  
Author(s):  
Daming Zhou ◽  
Helen ME Duyvesteyn ◽  
Cheng-Pin Chen ◽  
Chung-Guei Huang ◽  
Ting-Hua Chen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Economic Impact ◽  
Receptor Binding ◽  
Late Stage ◽  
Structural Basis ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Receptor Binding Site ◽  
Conserved Epitope

AbstractThe COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6Å crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues of this epitope are key to stabilising the pre-fusion Spike. Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19.

scholarly journals Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants

Science ◽  
2021 ◽  
pp. eabh1139
Author(s):  
Meng Yuan ◽  
Deli Huang ◽  
Chang-Chun D. Lee ◽  
Nicholas C. Wu ◽  
Abigail M. Jackson ◽  
...  
Keyword(s):  
South Africa ◽  
Binding Site ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Antigenic Drift ◽  
Spike Protein ◽  
Binding Modes ◽  
Next Generation ◽  
Wild Type ◽  
Receptor Binding Site

Neutralizing antibodies (nAbs) elicited against the receptor-binding site (RBS) of the spike protein of wild-type SARS-CoV-2 are generally less effective against recent variants of concern. RBS residues E484, K417 and N501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on ACE2 binding and K417N and E484K mutations on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternate binding modes, are abrogated by K417N, E484K, or both. These effects can be structurally explained by their extensive interactions with RBS nAbs. However, nAbs to the more conserved, cross-neutralizing CR3022 and S309 sites were largely unaffected. The results have implications for next-generation vaccines and antibody therapies.

scholarly journals Crystal Structure of the IL-10/IL-10R1 Complex Reveals a Shared Receptor Binding Site

Immunity ◽  
2001 ◽  
Vol 15 (1) ◽  
pp. 35-46 ◽  
Author(s):  
Kristopher Josephson ◽  
Naomi J. Logsdon ◽  
Mark R. Walter
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Receptor Binding ◽  
Receptor Binding Site
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