Fig. 6: Structure of the promoter specificity subunit gp226.
From: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
a Ribbon diagram of gp226 with regions structurally similar to bacterial σ factors colored in yellow green (helices 2.1 through 2.4 and 4.1) and gold (finger). The unique N- and C-terminal domains colored medium orchid. Residue numbers and identities are given at key locations. The DNA strands are colored as in Fig. 2a, b and are semitransparent. The pseudo−35-element binding motif is turquoise and its positively charged and solvent-exposed residues are shown in a stick representation. Inset: Conservation of residues comprising the 2.1bis helix. WebLogo78 shows a 2.1bis helix-centered fragment of a full-length multiple sequence alignment, calculated using ClustalX77, of twelve gp226 homologs currently available at GenBank. b Ribbon diagram of the E. coli σE factor (PDB code 6JBQ22) with its helix-turn-helix motif colored in orange red. Positively charged residues that interact with the DNA are shown in a stick representation and labeled. The DNA backbone is semitransparent. .
