Conserved motifs of the Orf6 protein. ( A ) Distribution of the Orf6-specific (inserts I and II) or Rpb1 (red) and Rpb2 (blue) conserved domains on the Orf6 amino acid chain, based on the sequence alignments provided as Supplementary Data S1 . ( B ) Spatial organization in the yeast RNAP II crystal structure (upper view). This figure is based on the 1R9S PDB coordinates showing the elongating RNAP II ( 8 ) using the same colour code and same orientation as in Figure 1 B above. Grey ovals denote the hypothetical insertion sites of the Orf6-specific domains. ( C ) Spatial organization of the conserved protrusion, fork, hybrid binding and switch 3 domains of Rpb2 on each side the RNA/DNA hybrid structure (side view). The orange, blue, grey and green spheres highlight positions 199–210 (protrusion), 466–512 (fork), 763–778 (hybrid binding) and 1106–1131 (switch 3) of yeast Rpb2, respectively. The first nine complementary bases of the RNA and template DNA strand are shown in red and blue, respectively.