Fig. 3

GPS proteins beneath the capsid shell. a Top, cut-through density of a virus facet viewed along the icosahedral three-fold axis; arrows and arrowheads indicate the density (shades of blue) beneath the three-tower (Nos. 1–3, see Fig. 1a center) and two-tower (Nos. 4 and 5) capsomers (black hexagons), respectively. The outer leaflet (OL) of the membrane is in lime-yellow. Below, schematic of the capsomers composing the facet with one IAU outlined by a thicker black line (represented as in Fig. 1a). Pentagons, triangles and ovals mark the icosahedral symmetry five-fold, three-fold, and two-fold axes. b Top, side-view of the Gaussian filtered (1.4 Å width in Chimera³⁵) electron density (white 40% transparency) corresponding to the three-tower capsomer No. 3 close to the icosahedral three-fold axis (as from schematic, top left corner) with further density beneath marked by a black rectangle with the GPS-III poly-ALA model fitted in (cyan cartoon) and in lime-yellow the blurred membrane OL; the same atomic model at the center shows an orthogonal view of the GPS-III protein with an inset of a stereoview of the density (gray mesh contoured at ∼2σ in Pymol) corresponding to the resolved strands (black rectangle). c As b but corresponding to the density of the two-tower capsomer No. 4 (as from schematic, top left corner) with the additional density at its center as marked by the black rectangle corresponding to the five-helix bundle GPS-II protein (green cartoon). d Top view along the pseudo-three fold axis of MCPs composing the three-tower capsomers as cartoon tube color-coded as Fig. 2a with the off-centered GPS-III protein represented in cyan surface; labels identify the VP7–VP4 subunits and curved black arrow with numbers the putative order of docking/registering of the VP7–VP4 subunits onto the GPS-III. e As d but for the two-tower capsomers where the GPS-II (green surface) is centered with the α₃ spanning the central cavity of the two-tower capsomers stapling together the opposite VP7–VP4 heterodimers (curved black lines) and leaving space for the docking of monomeric VP7