view article
Figure 4
Stabilization and deformation of the upstream B-form DNA by the σ-factor-like subunit GP68. (A) The upstream double-helical DNA up to the formation of the bubble is shown in overview within a transparent isosurface of the experimental map. Base numbering has been superimposed for orientation. (B) Complementation of the phosphate backbone in the region −17 to −24 by predominantly positively charged residues from GP68. The electrostatic isosurface is rendered transparently to illustrate the charge complementation of the phosphate backbone. Blue indicates positive charge, red negative and white neutral, and this colour scheme is preserved for all other electrostatic isosurfaces rendered within this article. (C) Complementation of the phosphate backbone in the region −12 to −24 by predominantly positively charged residues from GP68 and GP71-73. The electrostatic isosurface is rendered transparently to illustrate the charge complementation of the phosphate backbone. Panels (B) and (C) are rotated by 180° from one another as indicated between them. (D) Comparison of the naked p119L promoter analogue DNA with the position of the upstream B-form DNA bound by GP226 in the AR9 structure, which is somewhat similar in situation and conformation. DNA bound to the ΦKZ nvRNAP is shown in gold, while that bound to the AR9 nvRNAP is shown in cyan. (E) Comparison of the deformed DNA bound by the N-terminal domain of GP68 to idealized B-form helical DNA (shown in white), detailing the helix approaching the promoter bubble. Inset is an expanded view of the region indicated with dotted lines, highlighting the deformation from −8 to −11. All protein and DNA is visualized according to the Fig. 1[link] colour scheme unless otherwise stipulated.

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