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Figure 3
Schematic illustration of the binding elements from the ΦKZ nvRNAP interacting with the ΦKZ p119L open promoter analogue DNA. (A) The resolved region of the p119L open promoter analogue is shown as cartoon purine and pyrimidine bases in the standard DNA colour scheme (A: green, T: red, G: black, C: blue), with regions that are too weakly resolved to be modelled faded and lacking outlines. The p119L DNA sequence is shown in bold capitals, with the non-template strand above and template strand below, while the mismatches introduced to force bubble formation are shown in thin capitals. The 4 base-pair consensus sequence is shown in bold magenta text. Numbering is according to the transcription start site. The exposed bases in the region forming the bubble are shown with flipped out cartoons. Key interactions are shown through side chains connected to the relevant residue and protein name. Interactions with the phosphate backbone are shown reaching toward the appropriate letter in the sequence, while interactions with bases are shown contacting the relevant base cartoon. (B) DNA and contacting residues from panel (A) are shown within a transparent surface representation for ease of orientation. Stick representation is used with CPK colouring, and the labelling of individual residues is identical to that shown in panel (A).

IUCrJ
Volume 13| Part 1| January 2026| Pages 31-43
ISSN: 2052-2525
https://doi.org/10.1107/S2052252525009273