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. 2021 Jun 29;12:3889. doi: 10.1038/s41467-021-24151-3

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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. 2 — a Side-view of the AcrB trimer with the TM8/PC2 tunnel of the L2 protomer (blue) starting from the TM7/TM8 groove to the access pocket (AP), and ending at the entrance of the (closed) deep binding pocket (DBP) underneath the switch loop (magenta). b DDM (carbon, black; oxygen, red) binding to the TM8/PC2 tunnel with the tilted TM8 (magenta) and c-loop (green). The Polder electron density map (green mesh) assigned to DDM is contoured at 4.0 σ. c Conformational changes of tilted TM8/c-loop (L protomer, magenta; L2: red) and PC1/PC2 subdomains (L, orange; L2: yellow). Inset: DDM binding to the L protomer (white), L2 protomer (black), and DDM bound to an AcrB/erythromycin complex (PDB ID: 4ZJL¹⁶) (cyan). d Binding of fusidic acid (FUA) to the TM7/TM8 groove of AcrB-Phe380Ala. Inset: Polder electron density map (green mesh) assigned to FUA (carbon, black; oxygen, red) is contoured at 4.2 σ. e Binding of FUA to the TM7/TM8 groove in the T^FI-LIG2 (fully induced) protomer (carbon, black; oxygen, red). Polder map (green mesh) of FUA is contoured at 5.0 σ. f Superimposition of the TMD (TM5, TM7-10) of FUA bound to AcrB-Phe380Ala (yellow) and the AcrB T^FI-LIG2 (orange) T protomers.