Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins
(A) Structure of S1-NTD from α-genus human coronavirus NL63 (PDB ID: 5SZS). Although each subunit of NL63 S1 contains two copies of S1-NTDs (i.e., S1-NTD1 and S1-NTD2), S1-NTD2 was used in structural comparisons with the S1-NTDs from the other genera because it occupies the same location as the S1-NTDs from the other genera in quaternary structures of the spikes (see Fig 5A). (B) Structure of S1-NTD from δ-genus porcine delta coronavirus (PdCoV) (PDB ID: 6B7N). (C) Structure of S1-NTD from γ-genus IBV. (D) Structure of S1-NTD from β-genus SARS coronavirus (PDB ID: 5X58). * indicates sugar-binding site or putative sugar-binding site in sugar-binding S1-NTDs from each genus. Core structure, partial ceiling, and extensive ceiling are labeled. Arrows from panels (A) to (D) indicate evolutionary direction. (E) Quantitative structural comparisons among S1-NTDs from different genera using software Dali . Both Z-score and r.m.s.d. were calculated for each pair of the proteins. PDB IDs for NL63, PdCoV and SARS S1-NTDs are the same as in panels (A)-(D). PDB IDs for mouse hepatitis coronavirus (MHV) and MERS coronavirus are 3JCL and 5X5F, respectively. CEACAM1b (PDB ID: 5VST), whose β-sandwich fold is topologically different from that of coronavirus S1-NTDs , was used as a negative control. N.D.: no detectable structural similarity.