Class I GTP aptamer structure. (A) Ensemble of 10 lowest energy structures. Stereo view of the superimposed recognition bulge structures (residues 8–17, 29–34) overlaid on the average structure (gray). The residues are colored according to sequence conservation as in Figure 1: red = invariant, green = two-base varying, black = unconserved. The GTP ligand is colored blue, oriented with the disordered triphosphate region pointing upward. (B) Minimized average structure. Stereo view of the average structure of the converged ensemble after energy minimization. Nucleotides from the outer stem (P1) are colored orange. Nucleotides from the inner stem and UUCG tetraloop (P2) are colored green. Nucleotides from the 5′ strand of the recognition bulge (L1) are yellow. Nucleotides from the 3′ strand of the recognition bulge (L3) are purple. The GTP ligand is blue. The 5′ and 3′ ends of the aptamer are shown. The complex is rotated ~45° counterclockwise relative to the image in A. (C) Cartoon model of the Class I GTP aptamer. In this representation, the bottom stem is P1. The outlining corresponds to the colors in B (e.g., orange = P1 nucleotides, green = P2, etc.). The nucleotide positions are colored with circles as in Figure 1 according to sequence conservation: red = invariant positions, green = two-base varying positions, black = unconserved positions. The 5′ and 3′ ends are marked.
