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. 2024 Jan 10;15:417. doi: 10.1038/s41467-023-44637-6

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© The Author(s) 2024

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. 1 — a Substrate-induced occlusion of SERT leads to closure of the outer gate, represented as top) surface and bottom) cartoon. Transmembrane Helix 1 (TM1) and TM2, and TM6 and TM7 are highlighted in red and yellow, respectively. The dashed green line indicates the measured distance across the outer vestibule between TM6a and TM9up. b The insert of a shows the key interactions between serotonin (5HT) and SERT that trigger the motion of occlusion. c Top view of b highlighting the displacement of the bundle domain as the transporter moves from outward-open (OO) to outward-occluded (OC), while the scaffold as well as the substrate maintain their positions, coloured opaque and bright, respectively. The red and yellow arrows indicate the direction of TM1b and TM6a associated with SERT occlusion, respectively. d Structure of 5HT and its analogues methyl (M)-5HT, propyl (P)-5HT and butyl (B)-5HT. e Time evolution of the distance between TM6a and TM9up as a measure to quantify the degree of occlusion. Each of the six plots displays all ten replicas (n = 10) depicted in different colours (apo: shades of red, M-5HT: shades of peach, 5HT: shades of mauve, P-5HT: shades of cyber grape, B-5HT: shades of petrol, and cocaine (COC): shades of light blue). Dashed lines represent the openness of the outer gate by measuring the distances of the centre of mass from TM6a (residue G324 to L337) to centre of mass of TM9up (residue F475 to S477) from 3 known structures: 5I73 (outward open: OO), 6DZV (outward occluded: OC) and 6DZZ (inward open: IO)^18,29,34.