Model of PUF-11 interactions with RNA. The protein is depicted as a series of discs corresponding to PUF repeats, arranged in two groups of four. Interactions of bases (ellipse) with binding pockets in each repeat also are shown. Alternate conformations in the central region of the protein alter the overall curvature, as has been observed with FBF (Y. Wang, L. Opperman, M. Wickens, and T. Hall, in prep.), and affect base flipping. In one conformation, the protein is curved and the bases are “in,” contacting the protein (left, “Curved and In”). In the other conformation, the protein is flat and the central bases flip (right, “Flat and Flipped”). The alteration of structure may involve different helical packing in that region, rather than a distinct “hinge” region. See the text for details.
