The tertiary structure of the G-ribo motifs in the E. coli ribosome (Schuwirth et al. 2005). (A) Superposition of all cases of the G-ribo motif. Helices 1 and 2 are on the left and right, respectively. For each case of the motif, the backbone is shown by the curve of a particular color. Only the nucleotides of the zero layer are shown explicitly. For three motifs S521 (white), L1024 (red), and L2383 (magenta), which do not have the third helix, the backbone continues from position 0S to 0P. For cases S861 (orange), A1047 (blue), L1309 (yellow), L1642 (green), and L2323 (black), which contain the third helix, the latter is not shown. The positions of 0P, 0Q, and 0R are well superimposed in all cases (for 0R, due to the variability of its identity, the superposition deals only with the backbone). The position of 0S is more flexible than those of 0P, 0Q, and 0R. (B) The tertiary structure of motif S861. The backbone (blue curve). The four strands P, Q, R, and S are indicated. Layers: −1 (red), 0 (yellow), and +1 (green). Nucleotide −1T (blue). Unpaired nucleotides of the levels above +1 (gray). Noncanonical base-pair G858–U828 (magenta) on top of the arrangement forms the first base pair of the third helix. (C) The superposition of the arrangements in the +1 layer in different G-ribo motifs. For each motif, the same color is used as in A. The C1′ atom of each nucleotide is shown as a ball. Nucleotides +1S in L1642 and +1P in L1024, which do not follow the common pattern, are not shown (see the text). In motifs L1024, L2323, and L2383, nucleotide +1Q does not exist (see Fig. 3). Despite the variations in the structure of different +1 arrangements, the positions of the glycosidic bonds of the equivalent nucleotides in different G-ribo motifs are rather close.
