FIG. 7.

Path of model RNA around the edges of the dodecahedral cage and into the interior of the PaV capsid. The cage has been flattened into a 2D projection for graphic simplicity. A single-stranded RNA with 4,322 nucleotides (the sum of nucleotides in PaV RNA1 and RNA2) has been arranged so that every one of the 30 edges of the dodecahedral cage is occupied by an antiparallel duplex, as observed in the crystal structure. The strand runs from the 5′ end (solid blue circle), along all the edges of the cage, drops down into (and returns from) the interior of the capsid at 12 stalactites (solid red circles), and ends at the 3′ end (solid green circle). Two of the vertices (upper left and lower right) have four-way junctions, and the other 18 have three-way junctions. Of the latter, 7 have all three arms radiating out from the junction along the edges of the cage, whereas the other 11 have two arms on the cage and the third arm forms a stalactite. Eleven edges are occupied by stem-loops, with the RNA approaching the vertex with the stalactite, but then doubling back along the same edge, rather than passing through the vertex.