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. 2021 Dec 2;12:7018. doi: 10.1038/s41467-021-27305-5

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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. 6 — a PRE-INITIATION (dark grey, teal, dark blue, hot pink) and APO-RIBBON (light grey, light cyan, light blue) structures are superimposed. The pyramid and α-bundle rotations between apo- and promoter-bound structures are indicated as well as the 340-loop and the 860-region. Promoter RNA is shown in pink and orange. b Close-up of the interaction site between promoter RNA (pink and orange) and the pendant (hot pink), thumb-ring (yellow) and thumb (green) domains in the PRE-INITIATION structure. The pyramid domain is shown in teal. c Superposition of the PRE-INITIATION and APO-ENDO structures. PRE-INITIATION is presented as a transparent surface in grey with the pendant (hot pink) and α-bundle (blue) as well as the 5′ (pink) and 3′ (orange) vRNA highlighted in colour. The EN domain of the APO-ENDO structure is shown as an orange ribbon, which overlaps with the pendant domain volume of the PRE-INITIATION structure.