Volume 8, Issue 5, Pages 1137-1143 (November 2001) Structure of an Archaeal Homolog of the Eukaryotic RNA Polymerase II RPB4/RPB7 Complex  Flavia Todone, Peter Brick, Finn Werner, Robert O.J. Weinzierl, Silvia Onesti  Molecular Cell  Volume 8, Issue 5, Pages 1137-1143 (November 2001) DOI: 10.1016/S1097-2765(01)00379-3

Figure 1 Amino Acid Sequence Alignment for the RPB7 Homologs An alignment of the Methanococcus jannaschii (Metja) E subunit with the eukaryotic Saccharomyces cerevisiae (Yeast) and the human (Human) RPB7 subunits. Highlighted in magenta are the residues that are conserved in at least 15 of the 21 available archaeal and eukaryotic sequences; highlighted in green are the residues conserved in 9/12 archaeal homologs; and highlighted in yellow are the amino acids conserved in 7/9 eukaryotic sequences (the following couples of amino acid residues have been considered similar: Phe/Tyr, Asp/Glu; Ser/Thr, Arg/Lys). The position of the secondary structure elements in the E subunit is shown above the sequence. A dashed line indicates residues omitted from the final model. Molecular Cell 2001 8, 1137-1143DOI: (10.1016/S1097-2765(01)00379-3)

Figure 2 The Overall Structure of the E/F Complex (A) Stereo diagram showing a ribbon representation of the heterodimer. The E subunit (shown in blue) is an elongated molecule that folds into two domains: a β sheet (A) wrapped around a helix (K2) forms the N-terminal domain while the S1 motif in the C-terminal half of the protein folds into an antiparallel β barrel (B) with an OB-fold topology. The secondary structure elements that are part of the canonical S1 motif are shown in light blue. The disordered loop (residues 152 to 158) between strands B4 and B5 in the OB fold has been modeled for the sake of clarity and is shown as an orange dashed line. The F subunit (shown in magenta) folds into a series of helices that pack against one side of the E subunit at the interface between the two domains, with the N terminus contributing one strand to the N-terminal β sheet of E. (B) Schematic diagram showing the topology of the E/F complex. The secondary elements are colored and labeled as in (A). Molecular Cell 2001 8, 1137-1143DOI: (10.1016/S1097-2765(01)00379-3)

Figure 3 Surface Electrostatic Potential Mapping of the electrostatic potential on the surface of the E/F complex, with negative charges shown in red and positive charges in blue. On the left-hand side of the picture, the complex is shown in the same orientation as in Figure 2A (front), while on the right-hand side it is rotated by 180° around a vertical axis (back). The heterodimer shows a strikingly asymmetric charge distribution, with one side of the complex (particularly subunit F) highly negatively charged. Molecular Cell 2001 8, 1137-1143DOI: (10.1016/S1097-2765(01)00379-3)

Figure 4 Proposed Model for the Interaction of RPB4/RPB7 with the RNA Polymerase Core A schematic representation of the RNAPII 10 subunit core is shown (viewed in a similar orientation as the side view in Figures 3 and 6D of Cramer et al. (2000), with RPB5 shown in red and the mobile clamp, which closes onto the active side cleft upon nucleic acid binding, shown in green. The predicted exit path for the nascent RNA transcript is shown as a dashed line, and the proposed location of the heterodimer shown as a blue circle. The structure of the E/F complex is shown rotated by approximately 130° around a vertical axis with respect to the orientation used in Figure 2A. The position and orientation of the heterodimer is consistent with a wide range of structural and biological results, including low-resolution studies on 2D crystals and the positioning of the S1 motif binding face onto the nascent RNA transcript. The negatively charged surface of the F subunit is positioned on the outside, the insertion in the yeast RPB4 structure can be easily accommodated, and RPB7 plays the main role in the interaction, in agreement with the biochemical and genetic results. Molecular Cell 2001 8, 1137-1143DOI: (10.1016/S1097-2765(01)00379-3)