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. 2021 Jan 22;12:528. doi: 10.1038/s41467-020-20776-y

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a Comparison of the σ_1.2/σ_NCR and βlobe/Si1 conformations in apo-RNAP (middle), RPc (left), and RNAP-DksA/ppGpp (R-DksA, right, DNA is removed from the RP1-DksA/ppGpp to model this complex). RNAP (subunits and domains), DksA and DNA are indicated. Close-up views of the RNAP cleft are shown below. The DNA loading gate is closed in the apo-RNAP due to the βgate loop (βGL) contacts with σ_1.1/σ_1.2 (white dashed oval). The opening of the DNA loading gate in RPc and RP1-DksA/ppGpp is indicated by blue and red arrows, respectively. b A proposed model of σ_1.1 ejection in the RPc. The RPc is depicted as a transparent surface with cartoon models of the clamp (purple) and the lobe/Si1 (blue). The clamp in the apo-form RNAP and the lobe/Si1 in RP1-DksA/ppGpp are colored gray and white, respectively. In the RPc, the σ_NCR rotation (black arrow) contacts the β’CT, resulting in clamp movement toward σ_1.1 (red arrow) and a steric clash with σ_1.1 (white oval).