Figure 13-2: Structure of PRD1. Cryo-electron microscopy and image reconstruction of PRD1 at 1.4 nm resolution (A, B) reveal in central cross-section (A) the organisation of the virion into 3 layers, the outer protein capsid, the membrane bilayer and the underlying concentric DNA rings. The surface representation of the icosahedral virion reconstruction viewed down a 3-fold axis of symmetry shows the pseudo T=25 arrangement of the surface lattice (B). Spikes on the virion vertices that are sometimes evident in cryo-electron micrographs of the virion (arrow in C) are averaged out in the reconstruction, leaving only a small central bump as seen in the section (A) and on the surface representation (B), enlarged in (D). The vertex base (D) is made of a P31 pentamer which is similar in shape and dimensions when modelled from SAXS data of the recombinant protein (E, (63). (F) A ribbon diagram of the atomic model of the monomeric receptor binding protein, P2, (69). The pseudo beta-propeller head is the top domain, the extended ß-sheet tail is the bottom domain. (G) The atomic model of the trimeric major coat protein, P3, fits into 4 quasi-equivalent positions in the EM density (wire mesh from a 1.4 nm PRD1 P9- mutant reconstruction). The P3 C(alpha) chains are shown fitted into the wire mesh (57). The density of P3 is also outlined in white in the left half of the section in (A). (H) A ribbon diagram of the P3 trimer as seen from the outside of the virion. One monomer is highlighted to show the two adjacent ß-barrels. The FG1 loops lock adjacent monomers together, the FG2 helix lies in the subunit interface. (I) A side view of the P3 trimer rotated 90º relative to (H). The larger beta-barrel forms all of the 720 towers seen in the reconstruction (A, B). The I1B2 loop and the N and C termini all face the viral membrane (12). Scale bar in (A) 50 nm, in (C) 100 nm, in (G) 5 nm. In (E) the pseudoatoms are 0.19 nm in radius. Figure (A) was prepared with SPIDER (25), (B) with opendx, (E) with rasmol (62), (F) with O (36), (F), (G) and (H) with Molscript and Raster3D (38, 44).