Atlas of Interactions Between Decoration Proteins and Major Capsid Proteins of Coliphage N4

Abstract

Coliphage N4 is a representative species of the Schitoviridae family of bacteriophages. Originally structurally studied in 2008, the capsid structure was solved to 14 Å to reveal an interesting arrangement of Ig-like decoration proteins across the surface of the capsid. Herein, we present a high-resolution N4 structure, reporting a 2.45 Å map of the capsid obtained via single particle cryogenic-electron microscopy. Structural analysis of the major capsid proteins (MCPs) and decoration proteins (gp56 and gp17) of phage N4 reveals a pattern of interactions across the capsid that are mediated by structurally homologous domains of gp17. In this study, an analysis of the complex interface contacts allows us to confirm that the gp17 Ig-like decoration proteins of N4 are likely employed by the virus to increase the capsid's structural integrity.

Keywords: Ig-like decoration protein; bacteriophage N4; capsid decoration protein; cryo-electron microscopy.

Figure 1

The arrangement and variation of MCPs in the N4 capsid. (A) The cryo-EM density map (left, contour level 0.239) is compared to the atomic model of the N4 capsid with a smoothed van der Waals surface displayed (calculated in UCSF ChimeraX v1.8). The pentameric MCPs are coloured blue, and the hexameric MCPs are coloured green and yellow. The gp17 decoration proteins are coloured in shades of pink, according to their relative position on the capsid. The density for a putative water molecule in chain I is shown with the distance measured in UCSF ChimeraX (top panel, contour level 0.725). (B) Richardson diagram of an MCP coloured from N- (blue) to C-terminus (red). The domains of interest are highlighted and compared between chains A and I in green and blue, respectively. (C) Selected MCP interfaces were analysed in UCSF ChimeraX, and contact side chains involved in interactions are displayed where relevant. Arg-ring density is displayed at contour level 0.286. P-loop F’ refers to the P-loop of chain F from the adjacent ASU.

Figure 2

Decoration interactions with MCPs. (A) ASU and relative capsid surface map numbering convention (B) Richardson diagrams of decoration proteins gp17 coloured from N- (blue) to C-terminus (red). Gp17β is shown as a reciprocal of gp17γ. An overlay of the DII-DIII loop between gp17γ and gp17α is shown in the right panel. (C) A heatmap of buried surface area (Å2) is calculated in PISA against each decoration protein and each MCP. (reference for PISA) (D) A selection of gp17 interfaces. Highlighted MCP surfaces indicate decoration-contacting residues.