A predicted receptor-binding and critical neutralizing domain in S protein of the novel human coronavirus HCoV-EMC.

Dear Editor,

Most recently, Yuen and colleagues have prospected, in this journal, that the discovery of the novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) may be the beginning of another SARS-like pandemic and the research preparedness against this potential pandemic is an important precautionary strategy.

The rapid identification of HCoV-EMC that caused a SARS-like disease in Saudi Arabia is attributed to the success in discovery of the SARS coronavirus (SARS-CoV). Therefore, the knowledge gained from the research on SARS-CoV and the structures of its spike (S) protein may provide a useful template for identifying receptor for HCoV-EMC and developing vaccines against HCoV-EMC.

SARS-CoV S protein consists of S1 and S2 subunits (Fig. 1 a). The S1 subunit contains the receptor-binding domain (RBD, residues 318–510) responsible for its binding to the angiotensin-converting enzyme 2 (ACE2) receptor. We previously demonstrated that the RBD is also a critical neutralizing domain (CND), which could induce highly potent neutralizing antibody responses in the immunized animals and protect against SARS-CoV challenge.6, 7 Therefore, the immunogen containing this CND is expected to be effective SARS vaccine candidates.

Figure 1

Prediction of the RBD/CND in the HCoV-EMC S protein S1 subunit based on the RBD in SARS-CoV S protein. (a) Schematic representation of the SARS-CoV S protein. SP, signal peptide; RBD, receptor-binding domain; CND, critical neutralizing domain; FP, fusion peptide; HR, heptad repeat; TM, transmembrane domain; and CP, cytoplasm domain. The residue numbers of each region represent their positions in the S protein of SARS-CoV. (b) Alignment analysis of the sequence of the RBD/CND (residues 321–508) in the SARS-CoV S protein with the corresponding region (residues 377–662) in the HCoV-EMC S protein. The secondary structure assignments are listed above the primary sequence with β-sheets highlighted as arrows and α-helices highlighted by cylinders, respectively. The conserved cysteines are highlighted with red circles. (c) Crystal structures of the RBD/CND in SARS-CoV S protein S1 subunit (1) and predicted structure of RBD/CND in HCoV-EMC S protein S1 subunit (2). A core consists of a five-stranded anti-parallel β-sheet (β1–β4, β7) connecting with three short α-helices (αA–αC), and an extended loop contains two-stranded β-sheet (β5, β6). N* and C* stand for the N- and C-termini of RBD/CND, respectively.

Sequence alignment of the RBD/CND in SARS-CoV S with that of the corresponding region (residues 377–662) in HCoV-EMC S protein revealed that both fragments have low homology (14% identity and 38% similarity). However, the core domain consisting of β-sheets and α-helices in both fragments have higher homology (23% identity and 61% similarity). Strikingly, six cysteines are located at the same sites in both fragments (Fig. 1b), suggesting that they share conserved conformational structures.

Based on the X-ray crystal structure of the RBD/CND domain in the SARS-CoV S protein (PDB id: 2DD8), the structure of the corresponding region in the HCoV-EMC S protein was predicted using the Swiss-Model Workplace homology modeling server. The results indicate that like the RBD/CND domain in the SARS-CoV S protein,9, 11 the fragment of residues 377–662 in HCoV-EMC S protein also contains a core domain consisting of 5 β-sheets (β1–β4, β7) and 3 α-helices (αA–αC) and a long extended loop containing 2 anti-parallel β-sheets (β5–β6) (Fig. 1c). It has been demonstrated that the core in the RBD/CND domain of the SARS-CoV S protein is responsible for maintaining the overall conformation of the protein, while the extended loop is responsible for its binding with the receptor ACE2 or a neutralizing antibody.9, 11 These findings suggest that the region (residues 377–662) in HCoV-EMC S protein may also serve as a RBD/CND and can be used as a probe to identify HCoV-EMC's receptor and as an immunogen to design vaccines to prevent HCoV-EMC infection.

Potential conflicts of interest

No reported conflicts.