Fig 1.
Overall structure of IBV spike ectodomain in the pre-fusion conformation.
(A) Schematic drawing of IBV spike ectodomain. S1: receptor-binding subunit. S2: membrane-fusion subunit. GCN4-His6: GCN4 trimerization tag followed by His6 tag. S1-NTD: N-terminal domain of S1. S1-CTD: C-terminal domain of S1. CH: central helix. FP: fusion peptide. HR1 and HR2: heptad repeats 1 and 2. Residues in shaded regions (N-terminus, HR2, GCN4 tag, and His6 tag) were not included in the structural model. Question mark indicates that the exact location of FP is uncertain; the range of FP used for making figures is consistent with a previous structural study on β-genus mouse hepatitis coronavirus spike [18]. (B) Cryo-EM density maps of IBV spike ectodomain with atomic model fitted in. The maps have a contour of 7.5 σ. (C) Cryo-EM structure of IBV spike ectodomain in the pre-fusion conformation. Each of the monomeric subunits is colored differently. (D) Structure of a monomeric subunit in the pre-fusion conformation. The structural elements are colored in the same way as in panel (A). Dotted line indicates residues 702–710 that are missing in the structural model. All structures are viewed from the side.
Fig 2.
Detailed structure of IBV spike ectodomain.
(A) Schematic drawing of IBV S1. SD1: subdomain 1. SD2: subdomain 2. SD1’ and SD1”: two parts of SD1. SD2’ and SD2”: two parts of SD2. (B) Structure of monomeric S1. S1-NTD is colored in cyan. S1-CTD is colored in green. SD1 is colored in magenta. SD2 is colored in orange. * indicates putative sugar-binding site. Partial ceiling on top of the S1-NTD core is labeled. Putative receptor-binding motif loops (RBMs) in S1-CTD are also labeled. (C) Structure of trimeric S1. Three S1 subunits are colored differently. (D) Structure of monomeric S2. The structural elements are colored in the same way as in Fig 1A. (E) Structure of trimeric S2. Dotted line indicates residues 702–710 that are missing in the structural model. The structural elements of subunit A are colored in the same way as in Fig 1D. Subunits B and C are colored in light purple and light pink, respectively. All structures are viewed from the side.
Fig 3.
Structural comparisons of S1-NTDs from four coronavirus genera.
(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 [58]. 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 [59], was used as a negative control. N.D.: no detectable structural similarity.
Fig 4.
Structural comparisons of S1-CTDs from four coronavirus genera.
(A)-(D): Structures of S1-CTDs from different genera. Core structures and RBMs are labeled. (E) Quantitative structural comparisons among S1-CTDs from different genera. The PDB IDs are the same as those in Fig 3. Left right arrows from panels (A) to (D) indicate that evolution could go either way.
Fig 5.
Quaternary packing of S1 from four coronavirus genera.
(A)-(D) Structures of trimeric S1 from different genera. Three S1 subunits are colored differently. The PDB IDs are the same as those in Fig 3. All structures are viewed from the side.