Atomic model of RHDV capsid.

<p>(<b>A</b>) Modeling the NTA domain. The crystal structure of the VP60 S domain was fitted to and refined against the cryoEM map of RHDV. The S domains from quasi-equivalent VP60 monomers A, B and C, are colored red, yellow, and blue, respectively. Dashed arrows point to the N-terminal, T67 residues resolved in the crystal structures. A/B and C/C dimers are highlighted by dashed orange and pink polygons, respectively. Difference densities between the fitted models and cryoEM map, shown in dark-green around a 3-fold axis, were used to trace and build the NTA segments of VP60. The final pseudo-atomic model of the RHDV inner shell, including the NTA segments (green) around the 3-fold axis, is shown in ribbon form on the right. (<b>B</b>) CryoEM density reveals that the NTA segments of the B and C monomers extend to the proximal 3-fold axis and interact with each other. Densities corresponding to the A, B, and C monomers are colored red, yellow, and blue, respectively and those for the NTA domains are colored grey and are surrounded by a dashed cyan hexagon. (<b>C</b>, <b>D, E</b>) The match between the final model and the cryoEM map for the A/B capsomer in (<b>C</b>), for the C/C capsomer in (<b>D</b>) and for the whole virus in (<b>E</b>). The color scheme is that used in (<b>A</b>). In (<b>C</b>) and (<b>D</b>), the L1 loop at the top surface of capsomers A/B and C/C is labeled. In (<b>E</b>), the whole pseudo-atomic model of RHDV is shown in ribbon representation and fitted into the cryoEM map and viewed along a 5-fold axis. Black triangles and an ellipse mark the positions of two 3-fold axes and a single 2-fold axis, respectively. (<b>F</b>) Atomic models of three quasi-equivalent RHDV VP60 monomers, A (red), B (yellow), and C (blue). The three models, represented in ribbon form, are superimposed with the P domains aligned. Conformational differences among the three subunits are shown in schematic form at the right, which highlights alternative orientations that the S domains adopt relative to P.