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Figure 1
Overall structure of the ΦKZ nvRNAP bound to the ΦKZ p119L open promoter analogue. (A) Primary structure schematic for the ΦKZ nvRNAP protein complex. Key domains are highlighted and labelled. The β-like subunits, GP123 and GP71-73, are shown in lime green and chartreuse respectively, the β′-like subunits, GP55 and GP74, are shown in marine blue and cyan respectively, and the σ-like subunit, GP68, is shown in yellow. Template strand DNA is shown in purple, while non-template strand DNA is shown in magenta. This colour scheme is preserved for all figures showing the ΦKZ nvRNAP, while homologous subunits in the AR9 nvRNAP are shown according to an identical colour scheme to preserve orientation for the reader. (B) The paths of the template and non-template strands are shown without accompanying protein from the same perspective as in the panel below. Their low-resolution continuation and linkage are shown by dotted lines. Supplementary Figure 8 shows the density supporting this tracing, which is in agreement with our structure of the transcribing ΦKZ nvRNAP complex. (C) Top right panel: Overview of the ΦKZ nvRNAP–p119L open promoter analogue complex in surface representation. Left panel: side view of the complex in cartoon representation from the angle of the DNA entrance channel. Central panel: front view of the complex from the angle of the N-terminal domain of GP68. Right panel: Top view of the complex from the angle of the β-lobe of GP123. The rotations relating the central panel to the side panels are shown. (D) The transcribing ΦKZ nvRNAP complex is shown for comparison. Both this structure, and that in panel (E), are shown from the same perspective as the central panel of (C). (E) Comparison with the fork-DNA-bound crystal structure of the AR9 nvRNAP (see also Supplementary Figure 2).

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