Models of the plant PUM-HD bound to RNA. (A, B) Ribbon (left) and stick (right) models of the PUM-HDs of AtPUM2 (A) and Os01g62650 (B) bound to the RNA bases of Box 2 of the NRE (UUGUAUAU) that interact with Puf repeats 2 to 8. The RNA is shown as a ball-and-stick model. In the ribbon diagrams, the amino acid side chains that interact with the Watson-Crick edge of each base are shown in green, and those that provide potential stacking interactions are colored magenta. In the stick models, only the amino acid side chains that contact RNA bases are shown. The extended loop between repeat 7 and 8 is identified (*). (C, D) Sequence alignment of residues in helix 2 of repeats 1-8 that provide putative RNA contact sites on the concave surface of the PUM-HD of AtPum2 (C) and Os01g62650 (D). Numbers above the sequences represent the position of each amino acid each Puf repeat. Numbers in brackets refer to the position of the first amino acid in the complete AtPum2 and Os01g62650 polypeptide sequence. Boxes surround the amino acid residues at positions 12, 13 and 16. (E, F) Schematic diagram showing the protein:RNA contacts in the models of the AtPum2 (E) and Os01g62650 (F) PUM-HDs bound to the NRE1. Dotted lines indicate potential hydrogen bonds, dashed lines indicate potential stacking interactions, and ')))))' indicates potential van der Waals interactions. Distances between atoms indicated on the lines are indicated in Ångstroms.