Fig. 4

Interactions at the vertices. a Left, protein structure cartoon of HCIV-1 VP9 penton protein with the labeled jelly-roll strands; center, cartoon-tube representation of VP9 (rainbow coloring: N-terminus, blue; C-terminus, red) with inset showing a stereoview of the corresponding electron density region (as in Fig. 1b inset) marked by the black rectangle with in stick the residues F55, F75, Y55, and R146. b Five copies of VP9 models (yellow, magenta, cyan, green, and red) fitted into the corresponding HCIV-1 cryo-EM map (solid white and Gaussian filtered with 2.8 Å width) viewed perpendicular to the icosahedral five-fold axis. Inset on the left, view of the penton complex from the top (one VP9 subunit in red tube, the remaining four in white); inset on the right, the density region corresponding to the membrane protein plugging the membrane vesicle five-fold apices (contoured at higher threshold) and compatible with five copies of the C-terminal transmembrane helix of VP13 (brown tube; see below, Methods and Supplementary Figure 9a-b). c Heatmap depicting the hierarchical clustering (dendrogram on the left) where rows indicate the viral proteins detected according to their normalized abundance factor (NSAF) across the columns which represent the gel bands (arrowheads 1, 2, 3) cut from the representative native gel on the right (MK, markers in kDa). Color scale represents the intensity values as defined as I = log2 (NSAF) with blue = low abundance, red = high abundance. The orange and green rectangles mark, respectively, the clustering of the MCPs and the proteins composing the vertex complex with identified VP13 grouping closer to the vertex complex whereas proteins VP10 and VP12 are almost equidistant from the two major clusters. d View of the cryo-EM map as blue mesh (contoured as in Fig. 1b inset) viewed along the five-fold symmetry axis with fitted the Cα model of the penton in red and with one VP9 jelly-roll labeled as in a left; the dashed black circles mark the extra β-strands deriving from the above spike complex and that interact with the VP9 G strands