Fig. 2: Structure of the RNAPII pre-termination complex (type 1).

a Schematic representation of the EC-Rat1-Rai1 complex and the RNA sequences used in this study. Y, the indicated complex was observed in cryo-EM analysis; ND, not detected (Supplementary Fig. 17). b Structures of the type-1 and type-2 RNAPII-Rat1-Rai1 complexes. The composite maps were generated from the overall-masked maps and the Rat1-Rai-masked focused maps by Phenix⁶⁴. The maps are colored to match the structural models (gray, RNAP; green, Rat1, blue, Rai1; yellow, DNA; red, RNA). c Structure of the elongation complex (EC) engaged with Rat1-Rai1 at the RNA exit (the type-1 complex). The structural model is displayed in two orientations. RNAPII, template DNA, non-template DNA, RNA, Rat1, and Rai1 are colored gray (Rpb7 in brown), yellow, orange, green, and blue, respectively. Transparent surfaces of DNA/RNA, Rat1, and Rai1 are overlaid. d Close-up view of the Rpb7-Rat1 interface. e The Rat1-binding site overlaps with the binding sites of the elongation factors Spt5 and Spt6. The structural model of the type-1 complex is shown in transparent surface, colored as in (c). The structural model of RNAPII EC (PDB 7XN7) is superimposed with the type-1 complex by the Rpb1 subunit. Elongation factors Spt4, Spt5 and Spt6 are shown in cartoon representation and colored purple, blue, and pink, respectively. f The Rat1-binding site does not overlap with the binding sites of the Paf1 complex (Paf1, Leo1, Ctr9, Cdc73, and Rtf1), Elf1, and Spn1. The structural model of the type-1 complex is shown in transparent surface, colored as in (c). The structural model of RNAPII EC (PDB 7XN7) is superimposed with the type-1 complex by the Rpb1 subunit, and the elongation factors are shown in cartoon representation colored in light blue. g A close-up view of the interaction between the Rpb1 dock domain and the Rat1 α20 helix. Cryo-EM map (transparent surfaces) is overlaid on the structural model. h A close-up view of the interaction between the Rpb2 wall domain and the Rat1 α12 helix. The cryo-EM map (transparent surfaces) is overlaid on the structural model.