Fig. 5. The refined 3D model of the td intron. (A) The global view of the intron points to the importance of the loop E motif (balls and sticks in red) both in the organization of the P7 extension and to the contacts between stem P3 and the P6/P6a A-rich internal loop (balls and sticks in orange). The remainder of the P7 extension is colored in green. The P4-P6 domain is marked in blue, while the P9 extension is shown in yellow. Stems P3 and P8 as well as junction J8/7 are labeled in purple. The helices P1 and P2 are outlined in gray. (B) The structure of the eukaryotic loop E motif was taken from Correll et al. (1999). It is described using the nomenclature proposed in Leontis and Westhof (2001): squares indicate that the base interacts via the Hoogsteen edge, triangles via the sugar edge and circles via the Watson–Crick edge. Open symbols are used for trans and full symbols for cis orientations of the glycosidic bonds relative to the hydrogen bonds. The sheared A·G pair involves hydrogen bonding between N6 of A and N3 of G, and between N7 of A and N2 of G. In the universally conserved trans Watson–Crick–Hoogsteen U·A pair, N3 of U interacts with N7 of A, and O2 of U contacts N6 of A. The N1 position of the bulged guanine residue is likely to be hydrogen-bonded to the phosphate oxygen of the cross strand A of the A·A pair. The symmetrical pairing between the trans Hoogsteen–Hoogsteen A·A pair involves hydrogen-bonding of the N7 and N6 positions of one A to the N6 and N7 positions of the other A. A typical example of contacts between a loop E motif and an RNA helix taken from the 23S rRNA of Haloarcula marismortui (Ban et al., 2000) is shown to the left of the one built into the td model. The underlined bases indicate those making the shallow groove contact the loop E motif. (C) The contacts between P3 and J6/6a, and a typical example from the 23S rRNA (Ban et al., 2000), are represented in a secondary-like structure diagram. In J6/6a, the dotted triangles on either side of the A·A pairs are meant to convey that the precise nature of the interactions cannot be fixed at this stage.