Schematic representation of the Rpb1 segment between positions 375 and 1,493 ending with the carboxy-terminal repeated domain (CTD) beyond position 1,493, and the Rpb2 segment between positions 44 and 1,224 (S. cerevisiae numbering). The localization of the conserved domains defined by us is indicated (Dock_c, Funnel_c, Foot_c, Jaw_c and Wall_c). Thick black lines indicate the limit of the different RNAP II domains.1 Colored boxes correspond to the universally conserved α25 (bridge), α36, α37 (trigger loop), α46/47 helices and switch1/5 (Rpb1-α48-β34-α49) motifs. Striped boxes denote the Rpb1-β24/25 and rpb1-α44 motifs absent in the bacterial and chloroplastic enzymes. Contact between TFIIS, TFIIB, CE, Mvp1, Spo14 and Rpb1, as well as between TFIIB and Rpb2 are indicated. The main contacts between TFIIS and Rpb1 are indicated by black stars. Red thick lines denote the Rpb1 and Rpb2 α-amanitin binding sites.6

The conserved domains of the jaw, Jaw_c, and wall, Wall_c: Amino acid comparisons of Rpb1, Rpc160 and Rpa190 (for the Jaw_c) or Rpb2, Rpc128 and Rpa135 (for the Wall_c) and their orthologs in archaea and bacteria. Amino acids conserved only in RNAP II are shown in yellow. Other highly conserved positions are shown in red (when they were present in at least half of the compared sequences). The following AG, ST, CS, DN, DE, EQ, MILV, KR and FWY were grouped together. Species are indicated as follows: Sc (Saccharomyces cerevisiae), Sp (Schizosaccharomyces pombe), Hs (Homo sapiens), Mj (Methanococcus jannaschii), Ec (Escherichia coli) and Ta (Termus aquaticus). The amino acid residue numbers indicated correspond to S. cerevisiae Rpb1 or Rpb2 subunits. Boxes correspond to highly conserved groups of amino acids in the RNAP II sequences and only extended to one homologous sequence.

Spatial organization of the conserved domains of the RNAP II and TFIIS (PDB 1Y1V), (A) TFIIB (PDB 3K1F), (B) as well as localization of CE, MVP1 and SPO14 regulators over the structure of the RNAP II (PDB 1WCM), showing also the conserved domain of the foot (foot_c) (C).