The structural constraints predict a two-shell genome organization in bacteriophage MS2. (a) The outermost points of the best-fit array scale to the N-terminal β-hairpins of the capsid proteins in MS2 (magenta). (b), (c) Central sections through the particle; (b) illustrates the match to the crystal structure in surface representation (Valegård et al., 1990), with TR stem-loops shown in yellow. As can be seen in the close-up in (d), array points are located at the contact points between stem-loops and protein. This is even more striking given that yellow and orange points are predicted to be located at different radial levels, corresponding to the contacts with the two different types of dimeric building blocks (A/B and C/C) of the capsid. (c) An illustration of the match with the cryo-EM RNA density (Toropova et al., 2008), shown here as a radially coloured transparent surface. Array points map the inside (maroon points, radius of 38 Å) and outside (blue and mid-blue points, 62 and 65 Å, respectively) surfaces of the inner RNA shell, and also mark the density connecting the inner and outer RNA shells (cyan, 75 Å). Strikingly, magenta and maroon points together define the spatial extent of material in this particle.