Crystal Structure of the Receptor-Binding Domain from Newly Emerged Middle East Respiratory Syndrome Coronavirus

Abstract

The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) has infected at least 77 people, with a fatality rate of more than 50%. Alarmingly, the virus demonstrates the capability of human-to-human transmission, raising the possibility of global spread and endangering world health and economy. Here we have identified the receptor-binding domain (RBD) from the MERS-CoV spike protein and determined its crystal structure. This study also presents a structural comparison of MERS-CoV RBD with other coronavirus RBDs, successfully positioning MERS-CoV on the landscape of coronavirus evolution and providing insights into receptor binding by MERS-CoV. Furthermore, we found that MERS-CoV RBD functions as an effective entry inhibitor of MERS-CoV. The identified MERS-CoV RBD may also serve as a potential candidate for MERS-CoV subunit vaccines. Overall, this study enhances our understanding of the evolution of coronavirus RBDs, provides insights into receptor recognition by MERS-CoV, and may help control the transmission of MERS-CoV in humans. Since the summer of 2012, a novel coronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), has emerged from the Middle East and spread to parts of Europe. MERS-CoV infection often leads to acute pneumonia and renal failure, and the human fatality rate is more than 50% (1, 2). To date, MERS-CoV has infected at least 77 people and was able to be transmitted from human to human. The genomic sequence of MERS-CoV is closely related to the sequences of certain bat coronaviruses (3-5), raising concerns over persistent bat-to-human cross-species transmission of the virus. The clinical signs and epidemic patterns of MERS-CoV are reminiscent of the severe acute respiratory syndrome coronavirus (SARS-CoV), the etiological agent of the worldwide SARS epidemic in 2002-2003 that infected more than 8,000 people with a ϳ10% fatality rate (6, 7). MERS-CoV poses a significant threat to global health and economy.Coronaviruses are enveloped and positive-stranded RNA viruses and can be divided into three major genera, ␣, ␤, and ␥ (8). They mainly cause respiratory, gastrointestinal, and central nervous system diseases in mammals and birds. Coronaviruses recognize a variety of host receptors. Human NL63 respiratory coronavirus (HCoV-NL63) from ␣-genus and SARS-CoV from ␤-genus both recognize angiotensin-converting enzyme 2 (ACE2) as their host receptor (9, 10). Porcine respiratory coronavirus (PRCV) and some other coronaviruses from ␣-genus recognize aminopeptidase N (APN) (11, 12). Mouse hepatitis coronavirus (MHV) from ␤-genus recognizes carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) (13, 14), although certain MHV strains also recognize heparan sulfate (15, 16). Some coronaviruses from each of the three genera recognize sugars (17-20). MERS-CoV belongs to the ␤-genus and uses human dipeptidyl peptidase 4 (DPP4) as its host receptor (21). Receptor recognition is a major determinant of coronavirus host range and tropism.An envelope-anchored trimeric spike p...

Current advancements and potential strategies in the development of MERS-CoV vaccines

“…DPP4 is expressed on primary bronchiolar epithelial cells and regulates the activity of hormones and chemokines through proteolytic cleavage [12, 35]. Recent studies have solved the crystal structures of MERS-CoV S protein alone, or complexed with its receptor DPP4, and mapped the RBD of MERS-CoV to the residues covering 367–588 or 367–606, respectively [32, 36, 37]. According to the crystal structures, the RBD of MERS-CoV also contains the core and receptor-binding subdomains, with the receptor-binding motif consisting of 84 amino acids (from V484 to L567) that form a four-stranded antiparallel β-sheet (Figure 3B) [32, 36].…”

“…Recent studies have solved the crystal structures of MERS-CoV S protein alone, or complexed with its receptor DPP4, and mapped the RBD of MERS-CoV to the residues covering 367–588 or 367–606, respectively [32, 36, 37]. According to the crystal structures, the RBD of MERS-CoV also contains the core and receptor-binding subdomains, with the receptor-binding motif consisting of 84 amino acids (from V484 to L567) that form a four-stranded antiparallel β-sheet (Figure 3B) [32, 36]. Similar to other CoVs, the HR1 and HR2 of MERS-CoV form a 6-helix bundle believed to drive virion-cell membrane fusion, with three HR1 helices forming the central coiled-coil core and three HR2 chains surrounding the core in the HR1 side grooves [23, 38, 39].…”

“…Similar to other CoVs, the HR1 and HR2 of MERS-CoV form a 6-helix bundle believed to drive virion-cell membrane fusion, with three HR1 helices forming the central coiled-coil core and three HR2 chains surrounding the core in the HR1 side grooves [23, 38, 39]. Figure 4 describes the crystal structures of SARS-CoV and MERS-CoV RBD complexed with their respective receptors, and the major neutralizing epitopes on SARS-CoV RBD for the neutralizing monoclonal antibody against SARS-CoV [36, 40–42]. Understanding of these neutralizing epitopes in RBD of SARS-CoV will provide useful guidance for the identification of the neutralizing epitopes in MERS-CoV RBD and, hence designing RBD-based, neutralizing epitope-dependent vaccines against MERS-CoV.…”

“…The RBM is in yellow. (PDB ID: 4KQZ) [36]. (F) Crystal structure of MERS-CoV RBD (black) complexed with its receptor human DPP4 (blue) (PDB ID: 4KR0) [37].…”

Human polyclonal immunoglobulin G from transchromosomic bovines inhibits MERS-CoV in vivo

“…The MERS-CoV receptor dipeptidyl peptidase 4 (DPP4) (17) is a multifunctional transmembrane endopeptidase that cleaves a protein regulator of insulin and other peptide hormones (17)(18)(19). The MERS-CoV RBD has been cocrystallized with the human DPP4 (hDPP4) protein (20), and antibodies to the RBD neutralize coronaviruses in vitro (21)(22)(23)(24)(25)(26). In a mouse model of severe acute respiratory syndrome coronavirus (SARS-CoV) infection, vaccineinduced and passively transferred neutralizing antibodies have proven to be effective (27).…”