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. 2019 Apr 16;20(8):1876. doi: 10.3390/ijms20081876

Figure 1.

Figure 1

Paramecium bursaria Chlorella virus-1 (PBCV-1) capsomer structures and arrangements. (a) A ribbon diagram of the PBCV-1 major capsid protein (MCP) Vp54 (PDB ID 5TIP). The two jelly-rolls are colored in yellow (J1) and cyan (J2), respectively; (b) a ribbon diagram of the PBCV-1 capsomer displaying a pseudo-hexagonal shape. Individual double jelly-roll MCPs are color-coded with pink, jade green, and azure; (c) Isosurface rendering of PBCV-1 cryo-EM map (EMD 5378). Capsomers are colored based on their orientation in red, blue, green, cyan, and orange. The boundaries of one trisymmetron and one pentasymmetron are outlined in white. One asymmetric unit within one pentasymmetron is outlined in dashed white lines. The yellow dots present the steps for calculating the triangulation number (T number) with the h and k numbers labeled in yellow. One set of icosahedral symmetry symbols are labeled in red; (d) The magnified icosahedral 2-fold surface areas (outlined in yellow dashed line in (c)) and three selected capsomers (A, B, and C). To show their orientations, these three capsomers are labeled by yellow triangles where the vertices of the triangle point to the three higher jelly-roll surface loops; (e) A schematic diagram of showing the three selected capsomers in (d) for highlighting their orientations, charge distributions, and binding modes. The outlines of the capsomer are colored as the same color in (b) with J1 and J2 labeled. Three binding modes are labeled by 1, 2, and 3, close to the corresponding interfaces. Two side views of PBCV-1 capsomer electrostatic surfaces are presented on the sides of capsomer C pointing to their corresponding surface. The electrostatic surfaces are rendered by Chimera with a color scale from −1.0 to 1.0 kT/Å. Negatively and positively charged areas are colored in red and blue, respectively. (f) The electrostatic potential field lines between three selected PBCV-1 capsomers rendered by Visual Molecular Dynamics (VMD). Negatively and positively charged capsomer surface areas are colored with a scale from −1.0 to 1.0 kT/Å.