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. 2019 Sep 13;10:4175. doi: 10.1038/s41467-019-11977-1

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© The Author(s) 2019

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 — Superimpositions of AMP-PNP and LPS-bound sfLptB₂FGC structures. a AMP-PNP binding induces the conformational changes of LptB (NDBs). The helical domains of the dimeric LptB (AMP-PNP-bound sfLptB₂FGC) showed a rotational shift of ~12 Å in the anti-clockwise direction from the nucleotide-free state of dimeric LptB (LPS-bound sfLptB₂FGC). The LPS-bound sfLptB₂FGC is coloured in the same as Fig. 1. The AMP-PNP-bound sfLptB₂FGC is coloured in marine blue and AMP-PNP shows as spheres. b A top view of superimposed transmembrane helices of LPS-bound sfLptB₂FGC and AMP-PNP-bound sfLptB₂FGC complex. AMP-PNP binding induces the TM helices of AMP-PNP-bound sfLptB₂FGC to rotate in the anti-clockwise direction with the largest shift of ~10 Å from the nucleotide-free state (LPS-bound sfLptB₂FGC) towards the central channel. c Slab view of surface representation of cavity of LPS-bound sfLptB₂FG. The cavity is in an outward open conformation. d Slab view of cavity of LPS-bound sfLptB₂FGC. The cavity is in an outward open conformation. The transmembrane helix of LptC is located at the lateral gate TM1G/TM5F, enlarging the cavity. The neck of the cavity is widely open. e Slab view of cavity of AMP-PNP-bound sfLptB₂FGC. The cavity is closed, which is induced by AMP-PNP binding