Molecular basis of differential receptor usage for naturally occurring CD55-binding and -nonbinding coxsackievirus B3 strains

Figures

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  Fig. 1.. Amino acid probability distribution of CVB3 surface proteins. (A–C) CVB3 sequences (n = 115) were collected and aligned. Of the 115 sequences, 95 were available in the NCBI database and 20 were isolates collected from China from 2012 to 2017. Amino acid probability distribution on each site of VP1 (A), VP2 (B), and VP3 (C) proteins. Variable residue sites are colored in red. (D and E) Percentage of CVB3 isolates according to the VP3-234 amino acid (Q/N//V/D/E) distribution (D) among 65 strains in Asia and other parts of the world (mainly Europe, the United States, and Australia) among 24 strains (E).

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  Fig. 2.. Direct binding of CD55 or CAR to CVB3 isolates. (A–F) BIAcore diagrams of the soluble extracellular domain of CD55 bound to CVB3E (A), CVB3D (B), CVB3V (C), CVB3N (D), and CVB3Q (E) full particles at pH 7.4, with empty particles of CVB3Q as control (F). (G–L) BIAcore diagram of the soluble extracellular D1D2 domain of CAR bound to CVB3E (G), CVB3D (H), CVB3V (I), CVB3N (J), and CVB3Q (K) full particles at pH 7.4, with empty particles of CVB3Q (L) as control. KD values were calculated using BIAcore 3000 analysis software (BIAevaluation version 4.1) and the fitting curves were labeled with a gray dotted line.

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  Fig. 3.. Cryo-EM structures and detailed interactions among CVB3 viral particles and the CD55 receptor. (A and B) Density maps of CVB3Q (3.0 Å), CVB3N (2.7 Å), and CVB3E (2.5 Å) full particles (A), and complexes CVB3Q–CD55 (3.2 Å) and CVB3N–CD55 (3.0 Å) (B) at pH 7.4. The density map is colored by radius, as indicated in the legend bar. (C) Atomic model of the CVB3_CD55 three main contact interfaces, I, II, and III, indicated by a dashed rectangle in black, magenta, and green, respectively. The receptor is shown in ribbon models, and the viral protein is represented in surface models. (D) Interaction details between CVB3Q or CVB3N and CD55. (E) Hydrogen-bond interactions between A122 of CD55 with CVB3Q or CVB3N. Presumptive interaction of A122 of CD55 with VP3-234E, VP3-234V, and VP3-234D. VP3-234E or VP3-234D residues have the same electric charge as the A122 carbonyl group of CD55, marked δ−. Interaction residues are shown in stick representation and hydrogen bonds are indicated by black dashed lines.

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  Fig. 4.. Cryo-EM structures of the complex CVB3–CAR and structural changes surrounding the pocket. (A–D) Cryo-EM maps of the CVB3Q–CAR complex incubated for 10 min at pH 7.4 (3.2 Å), and an additional 10 min at pH 7.4 (3.2 Å) or 5.5 (2.8 Å) (A). The density map is colored by radius, as indicated by the legend bar. Close-up view of the pocket factor inside the CAR-bound CVB3Q particle for 10 min (B) and the corresponding pocket site in the group, with an additional 10-min incubation at both pHs (C and D). (E and F) Cryo-EM maps (E) of CVB3E–CAR complex incubation for 10 min (3.7 Å) and an additional 10-min incubation at pH 7.4 (2.2 Å). Close-up view of the pocket factor when the pocket is missing (F). (G and I) Conformational changes in the pocket region of CAR bound to CVB3Q (G) or CVB3E (I) particles upon 10- and 20-min incubations at pH 7.4. (H and J) Enlarged views of the major residues including N211, N212, and M213, highlighting the conformational change in the pocket region of the CVB3Q (H) and CVB3E (J) capsids.