Switching of Receptor Binding Poses between Closely Related Enteroviruses

Figures

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  Figure 1. Overall structure of E11-DAF complex. (a) FSC curve of the E11-DAF complex with the threshold 0.143, the final resolution is 3.1 Å (calculated by Relion). (b) FSC curve of the local refined map centred at DAF with the threshold 0.143, the overall resolution is 3.9 Å (calculated by Cryosparc). (c) Representative density of E11 viral capsid. (d) Local resolution map of E11-DAF complex. (e) Three-dimensional reconstruction of E11-DAF complex with fitted DAF shown as cartoon. (f) Close-up of the Cryo-EM reconstruction of the E11-DAF complex, showing density for two DAF molecules (orange and red) related by icosahedral 2-fold. Note, domains SCR 2 and 3 of these two DAF molecules clash with each other. (g) Superimposition of the E11 bound DAF (orange) with that determined by crystallography (green, PDB: 1OK3). (h) Density of the pocket factor.

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  Figure 2. Interactions of E11 and DAF. (a) Roadmap [31] showing the residues of E11 involved in E11-DAF protein interactions. (b) SCRs 3 and 4 of DAF (orange), and the VP2 EF loop (green)and VP3 BC loop (red) of E11 are involved in E11-DAF interactions. The viral protomer is drawn as surface representation with the two loops involved in contacts with DAF shown as coils. VP1, 2 and 3 of E11 are colored in blue, green and red, respectively. (c) Binding residues at the E11-DAF interface (E11: VP2 green, VP3 red, DAF orange). Side chains of E11 are shown as grey sticks and those of DAF shown as yellow sticks; (d) Density showing contact between the Glycan attached to residue N95 of DAF (shown as a magenta circle) and residue K73 of VP2 (marked with a green circle).

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  Figure 3. Binding mode of DAF. (a) Two different binding patterns of DAF with different enteroviruses. The viral capsid is shown as surface representation, one pit region in the canyon region of the capsid is marked by a dashed circle and the outer rim of the canyon is marked by a larger dashed circle. DAF molecules are shown in cartoon representation with different colors indicating the different viruses they bound with (green: CVB3, PDB: 7VY5; yellow: E6, PDB:6ILK; red: E30, PDB:7C9W; cyan: E7, PDB:3IYP; orange: E11, structure in this paper; magenta: E12, PDB:1UPN). (b) Phylogenetic tree of 6 DAF binding enteroviruses based on the capsid structures. (c) Phylogenetic tree of 20 DAF-binding enteroviruses based on the capsid sequences (colours as in (a)). (d) Substitutions of VP2 G162 (left panel in green) conserved in viruses with E11 DAF binding mode with D/N/E (second to forth panel, respectively) found in viruses with E6 DAF binding mode would clash with S33 of DAF (orange). (e) Gene sequence alignment of 20 DAF-binding enteroviruses. Key residues for the E11 and E6 interactions are listed above and below the sequence alignment, respectively and those marked in red are conserved among…