{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T19:28:49Z","timestamp":1793647729284,"version":"4.5.1"},"reference-count":88,"publisher":"Springer Science and Business Media LLC","issue":"8025","license":[{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2024,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement<jats:sup>1<\/jats:sup>. Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, the human dopamine transporter (hDAT) and mechanisms by which it is inhibited by small molecules and Zn<jats:sup>2+<\/jats:sup> are without a high-resolution structural context. Here we determine the structure of hDAT in a tripartite complex with the competitive inhibitor and cocaine analogue, (\u2013)-2-\u03b2-carbomethoxy-3-\u03b2-(4-fluorophenyl)tropane<jats:sup>2<\/jats:sup> (\u03b2-CFT), the non-competitive inhibitor MRS7292<jats:sup>3<\/jats:sup> and Zn<jats:sup>2<\/jats:sup><jats:sup>+<\/jats:sup> (ref. <jats:sup>4<\/jats:sup>). We show how \u03b2-CFT occupies the central site, approximately halfway across the membrane, stabilizing the transporter in an outward-open conformation. MRS7292 binds to a structurally uncharacterized allosteric site, adjacent to the extracellular vestibule, sequestered underneath the extracellular loop 4 (EL4) and adjacent to transmembrane helix 1b (TM1b), acting as a wedge, precluding movement of TM1b and closure of the extracellular gate. A Zn<jats:sup>2+<\/jats:sup> ion further stabilizes the outward-facing conformation by coupling EL4 to EL2, TM7 and TM8, thus providing specific insights into how Zn<jats:sup>2+<\/jats:sup> restrains the movement of EL4 relative to EL2 and inhibits transport activity.<\/jats:p>","DOI":"10.1038\/s41586-024-07739-9","type":"journal-article","created":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T16:14:48Z","timestamp":1723047288000},"page":"672-677","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":66,"title":["Structure of the human dopamine transporter and mechanisms of inhibition"],"prefix":"10.1038","volume":"632","author":[{"given":"Dushyant Kumar","family":"Srivastava","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vikas","family":"Navratna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dilip K.","family":"Tosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Chinn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md Fulbabu","family":"Sk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8434-1010","authenticated-orcid":false,"given":"Emad","family":"Tajkhorshid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8104-1493","authenticated-orcid":false,"given":"Kenneth A.","family":"Jacobson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8549-2360","authenticated-orcid":false,"given":"Eric","family":"Gouaux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,7]]},"reference":[{"key":"7739_CR1","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.tins.2007.03.006","volume":"30","author":"A Bjorklund","year":"2007","unstructured":"Bjorklund, A. & Dunnett, S. B. Dopamine neuron systems in the brain: an update. Trends Neurosci. 30, 194\u2013202 (2007).","journal-title":"Trends Neurosci."},{"key":"7739_CR2","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1021\/jm00269a600","volume":"16","author":"RL Clarke","year":"1973","unstructured":"Clarke, R. L. et al. Compounds affecting the central nervous system. 4. 3 Beta-phenyltropane-2-carboxylic esters and analogs. J. Med. Chem. 16, 1260\u20131267 (1973).","journal-title":"J. Med. Chem."},{"key":"7739_CR3","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1124\/jpet.115.229666","volume":"357","author":"A Janowsky","year":"2016","unstructured":"Janowsky, A., Tosh, D. K., Eshleman, A. J. & Jacobson, K. A. Rigid adenine nucleoside derivatives as novel modulators of the human sodium symporters for dopamine and norepinephrine. J. Pharm. Expt. Therapeutics 357, 24\u201335 (2016).","journal-title":"J. Pharm. Expt. Therapeutics"},{"key":"7739_CR4","doi-asserted-by":"publisher","first-page":"4266","DOI":"10.1093\/emboj\/17.15.4266","volume":"17","author":"L Norregaard","year":"1998","unstructured":"Norregaard, L., Fredericksen, D., Nielsen, E. O. & Gether, U. Delineation of an endogenous zinc-binding site in the human dopamine transporter. EMBO J. 17, 4266\u20134273 (1998).","journal-title":"EMBO J."},{"key":"7739_CR5","doi-asserted-by":"publisher","first-page":"735","DOI":"10.3390\/cells10040735","volume":"10","author":"L Speranza","year":"2021","unstructured":"Speranza, L., di Porzio, U., Viggiano, D., de Donato, A. & Volpicelli, F. Dopamine: the neuromodulator of long-term synaptic plasticity, reward and movement control. Cells 10, 735 (2021).","journal-title":"Cells"},{"key":"7739_CR6","doi-asserted-by":"publisher","first-page":"107392","DOI":"10.1016\/j.pharmthera.2019.07.003","volume":"203","author":"C Bucolo","year":"2019","unstructured":"Bucolo, C., Leggio, G. M., Drago, F. & Salomone, S. Dopamine outside the brain: the eye, cardiovascular system and endocrine pancreas. Pharmacol. Ther. 203, 107392 (2019).","journal-title":"Pharmacol. Ther."},{"key":"7739_CR7","unstructured":"Kandel, E. R., Schwartz, J. H.and Jessel, T. M. Principles of Neural Science (Appleton and Lange, 1991)."},{"key":"7739_CR8","doi-asserted-by":"publisher","first-page":"a008862","DOI":"10.1101\/cshperspect.a008862","volume":"1","author":"CG Goetz","year":"2011","unstructured":"Goetz, C. G. The history of Parkinson\u2019s disease: early clinical descriptions and neurological therapies. Cold Spring Harb. Perspect. Med. 1, a008862 (2011).","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"7739_CR9","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1007\/s10571-018-0632-3","volume":"39","author":"MO Klein","year":"2019","unstructured":"Klein, M. O. et al. Dopamine: functions, signaling, and association with neurological diseases. Cell. Mol. Neurobiol. 39, 31\u201359 (2019).","journal-title":"Cell. Mol. Neurobiol."},{"key":"7739_CR10","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1007\/7854_2022_330","volume":"57","author":"MJ Groom","year":"2022","unstructured":"Groom, M. J. & Cortese, S. Current pharmacological treatments for ADHD. Curr. Top. Behav. Neurosci. 57, 19\u201350 (2022).","journal-title":"Curr. Top. Behav. Neurosci."},{"key":"7739_CR11","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1146\/annurev-pharmtox-030220-124205","volume":"61","author":"AH Newman","year":"2021","unstructured":"Newman, A. H., Ku, T., Jordan, C. J., Bonifazi, A. & Xi, Z. X. New drugs, old targets: tweaking the dopamine system to treat psychostimulant use disorders. Annu. Rev. Pharmacol. Toxicol. 61, 609\u2013628 (2021).","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"key":"7739_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s00424-013-1410-1","volume":"466","author":"G Rudnick","year":"2014","unstructured":"Rudnick, G., Kr\u00e4mer, R., Blakely, R. D., Murphy, D. L. & Verrey, F. The SLC6 transporters: perspectives on structure, functions, regulation, and models for transporter dysfunction. Pflugers Arch. 466, 25\u201342 (2014).","journal-title":"Pflugers Arch."},{"key":"7739_CR13","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1038\/180134a0","volume":"180","author":"P Mitchell","year":"1957","unstructured":"Mitchell, P. A general theory of membrane transport from studies of bacteria. Nature 180, 134\u2013136 (1957).","journal-title":"Nature"},{"key":"7739_CR14","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-30154-5","volume":"13","author":"SG Schmidt","year":"2022","unstructured":"Schmidt, S. G. et al. The dopamine transporter antiports potassium to increase the uptake of dopamine. Nat. Commun. 13, 2446 (2022).","journal-title":"Nat. Commun."},{"key":"7739_CR15","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.jneumeth.2005.11.014","volume":"154","author":"CJ Frederickson","year":"2006","unstructured":"Frederickson, C. J. et al. Synaptic release of zinc from brain slices: factors governing release, imaging, and accurate calculation of concentration. J. Neurosci. Methods 154, 19\u201329 (2006).","journal-title":"J. Neurosci. Methods"},{"key":"7739_CR16","doi-asserted-by":"publisher","first-page":"3109","DOI":"10.1021\/acs.jmedchem.7b00141","volume":"60","author":"DK Tosh","year":"2017","unstructured":"Tosh, D. K. et al. Scaffold repurposing of nucleosides (adenosine receptor agonists): enhanced activity at the human dopamine and norepinephrine sodium symporters. J. Med. Chem. 60, 3109\u20133123 (2017).","journal-title":"J. Med. Chem."},{"key":"7739_CR17","doi-asserted-by":"publisher","first-page":"3718","DOI":"10.1021\/acschemneuro.9b00262","volume":"10","author":"S Aggarwal","year":"2019","unstructured":"Aggarwal, S. et al. Identification of a novel allosteric modulator of the human dopamine transporter. ACS Chem. Neurosci. 10, 3718\u20133730 (2019).","journal-title":"ACS Chem. Neurosci."},{"key":"7739_CR18","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1038\/nature12533","volume":"503","author":"A Penmatsa","year":"2013","unstructured":"Penmatsa, A., Wang, K. H. & Gouaux, E. X-ray structure of dopamine transporter elucidates antidepressant mechanism. Nature 503, 85\u201390 (2013).","journal-title":"Nature"},{"key":"7739_CR19","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1038\/nature14431","volume":"521","author":"KH Wang","year":"2015","unstructured":"Wang, K. H., Penmatsa, A. & Gouaux, E. Neurotransmitter and psychostimulant recognition by the dopamine transporter. Nature 521, 322\u2013327 (2015).","journal-title":"Nature"},{"key":"7739_CR20","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nsmb.3029","volume":"22","author":"A Penmatsa","year":"2015","unstructured":"Penmatsa, A., Wang, K. H. & Gouaux, E. X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine. Nat. Struct. Mol. Biol. 22, 506\u2013508 (2015).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"7739_CR21","doi-asserted-by":"publisher","first-page":"e0200085","DOI":"10.1371\/journal.pone.0200085","volume":"13","author":"V Navratna","year":"2018","unstructured":"Navratna, V., Tosh, D. K., Jacobson, K. A. & Gouaux, E. Thermostabilization and purification of the human dopamine transporter (hDAT) in an inhibitor and allosteric ligand bound conformation. PLoS ONE 13, e0200085 (2018).","journal-title":"PLoS ONE"},{"key":"7739_CR22","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1124\/pr.108.000869","volume":"63","author":"AS Kristensen","year":"2011","unstructured":"Kristensen, A. S. et al. SLC6 neurotransmitter transporters: structure, function and regulation. Pharmacol. Rev. 63, 585\u2013640 (2011).","journal-title":"Pharmacol. Rev."},{"key":"7739_CR23","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1007\/978-3-031-21054-9_4","volume":"30","author":"S Aggarwal","year":"2023","unstructured":"Aggarwal, S. & Mortensen, O. V. Discovery and development of monoamine transporter ligands. Adv. Neurobiol. 30, 101\u2013129 (2023).","journal-title":"Adv. Neurobiol."},{"key":"7739_CR24","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1111\/jnc.15145","volume":"157","author":"K Jayaraman","year":"2021","unstructured":"Jayaraman, K. et al. SLC6 transporter oligomerization. J. Neurochem. 157, 919\u2013929 (2021).","journal-title":"J. Neurochem."},{"key":"7739_CR25","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nature03978","volume":"437","author":"A Yamashita","year":"2005","unstructured":"Yamashita, A., Singh, S. K., Kawate, T., Jin, Y. & Gouaux, E. Crystal structure of a bacterial homologue of Na+\/Cl\u2212 dependent neurotransmitter transporters. Nature 437, 215\u2013223 (2005).","journal-title":"Nature"},{"key":"7739_CR26","doi-asserted-by":"publisher","first-page":"32616","DOI":"10.1074\/jbc.M110.150565","volume":"285","author":"WC Hong","year":"2010","unstructured":"Hong, W. C. & Amara, S. G. Membrane cholesterol modulates the outward facing conformation of the dopamine transporter and alters cocaine binding. J. Biol. Chem. 285, 32616\u201332626 (2010).","journal-title":"J. Biol. Chem."},{"key":"7739_CR27","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1111\/jnc.12007","volume":"123","author":"KT Jones","year":"2012","unstructured":"Jones, K. T., Zhen, J. & Reith, M. E. Importance of cholesterol in dopamine transporter function. J. Neurochem. 123, 700\u2013715 (2012).","journal-title":"J. Neurochem."},{"key":"7739_CR28","doi-asserted-by":"publisher","first-page":"e1005907","DOI":"10.1371\/journal.pcbi.1005907","volume":"14","author":"T Zeppelin","year":"2018","unstructured":"Zeppelin, T., Ladefoged, L. K., Sinning, S., Periole, X. & Schiott, B. A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition. PLoS Comput. Biol. 14, e1005907 (2018).","journal-title":"PLoS Comput. Biol."},{"key":"7739_CR29","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1038\/nature17629","volume":"532","author":"JA Coleman","year":"2016","unstructured":"Coleman, J. A., Green, E. M. & Gouaux, E. X-ray structures and mechanism of the human serotonin transporter. Nature 532, 334\u2013339 (2016).","journal-title":"Nature"},{"key":"7739_CR30","doi-asserted-by":"publisher","first-page":"21012","DOI":"10.1074\/jbc.M311972200","volume":"279","author":"LB Li","year":"2004","unstructured":"Li, L. B. et al. The role of N-glycosylation in function and surface trafficking of the human dopamine transporter. J. Biol. Chem. 279, 21012\u201321020 (2004).","journal-title":"J. Biol. Chem."},{"key":"7739_CR31","doi-asserted-by":"publisher","first-page":"13419","DOI":"10.1073\/pnas.212519299","volume":"99","author":"PJ Reeves","year":"2002","unstructured":"Reeves, P. J., Callewaert, N., Contreras, R. & Khorana, H. G. Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl Acad. Sci. USA 99, 13419\u201313424 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7739_CR32","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/S0376-8716(99)00005-8","volume":"56","author":"MJ Kuhar","year":"1999","unstructured":"Kuhar, M. J. et al. Studies of selected phenyltropanes at monoamine transporters. Drug Alcohol Depend. 56, 9\u201315 (1999).","journal-title":"Drug Alcohol Depend."},{"key":"7739_CR33","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1016\/S0006-3223(99)00291-7","volume":"47","author":"EH Wong","year":"2000","unstructured":"Wong, E. H. et al. Reboxetine: a pharmacologically potent, selective, and specific norepinephrine reuptake inhibitor. Biol. Psychiatry 47, 818\u2013829 (2000).","journal-title":"Biol. Psychiatry"},{"key":"7739_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/srep15650","volume":"5","author":"J Andersen","year":"2015","unstructured":"Andersen, J., Ringsted, K. B., Bang-Andersen, B., Stromgaard, K. & Kristensen, A. S. Binding site residues control inhibitor selectivity in the human norepinephrine transporter but not in the human dopamine transporter. Sci. Rep. 5, 15650 (2015).","journal-title":"Sci. Rep."},{"key":"7739_CR35","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1016\/S0006-3223(01)01145-3","volume":"50","author":"MJ Owens","year":"2001","unstructured":"Owens, M. J., Knight, D. L. & Nemeroff, C. B. Second-generation SSRIs: human monoamine transporter binding profile of escitalopram and R-fluoxetine. Biol. Psychiatry 50, 345\u2013350 (2001).","journal-title":"Biol. Psychiatry"},{"key":"7739_CR36","doi-asserted-by":"publisher","first-page":"7124","DOI":"10.1016\/S0021-9258(17)37256-3","volume":"269","author":"H Gu","year":"1994","unstructured":"Gu, H., Wall, S. C. & Rudnick, G. Stable expression of biogenic amine transporters reveals differences in inhibitor sensitivity, kinetics, and ion dependence. J. Biol. Chem. 269, 7124\u20137130 (1994).","journal-title":"J. Biol. Chem."},{"key":"7739_CR37","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/nature12648","volume":"503","author":"H Wang","year":"2013","unstructured":"Wang, H. et al. Structural basis for action by diverse antidepressants on biogenic amine transporters. Nature 503, 141\u2013145 (2013).","journal-title":"Nature"},{"key":"7739_CR38","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/nature08143","volume":"459","author":"H Krishnamurthy","year":"2009","unstructured":"Krishnamurthy, H., Piscitelli, C. L. & Gouaux, E. Unlocking the molecular secrets of sodium-coupled transporters. Nature 459, 347\u2013355 (2009).","journal-title":"Nature"},{"key":"7739_CR39","doi-asserted-by":"publisher","first-page":"7782","DOI":"10.1073\/pnas.89.16.7782","volume":"89","author":"S Kitayama","year":"1992","unstructured":"Kitayama, S. et al. Dopamine transporter site-directed mutations differentially alter substrate transport and cocaine binding. Proc. Natl Acad. Sci. USA 89, 7782\u20137785 (1992).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7739_CR40","doi-asserted-by":"publisher","first-page":"16096","DOI":"10.1074\/jbc.272.26.16096","volume":"272","author":"Y Bismuth","year":"1997","unstructured":"Bismuth, Y., Kavanaugh, M. P. & Kanner, B. I. Tyrosine 140 of the gamma-aminobutyric acid transporter GAT-1 plays a critical role in neurotransmitter recognition. J. Biol. Chem. 272, 16096\u201316102 (1997).","journal-title":"J. Biol. Chem."},{"key":"7739_CR41","doi-asserted-by":"publisher","first-page":"eabl3857","DOI":"10.1126\/sciadv.abl3857","volume":"7","author":"D Yang","year":"2021","unstructured":"Yang, D. & Gouaux, E. Illumination of serotonin transporter mechanism and role of the allosteric site. Sci. Adv. 7, eabl3857 (2021).","journal-title":"Sci. Adv."},{"key":"7739_CR42","doi-asserted-by":"publisher","first-page":"e2304602120","DOI":"10.1073\/pnas.2304602120","volume":"120","author":"D Yang","year":"2023","unstructured":"Yang, D., Zhao, Z., Tajkhorshid, E. & Gouaux, E. Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Proc. Natl Acad. Sci. USA 120, e2304602120 (2023).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7739_CR43","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nature03978","volume":"437","author":"A Yamashita","year":"2005","unstructured":"Yamashita, A., Singh, S. K., Kawate, T., Jin, Y. & Gouaux, E. Crystal structure of a bacterial homologue of Na+\/Cl\u2212-dependent neurotransmitter transporters. Nature 437, 215\u2013223 (2005).","journal-title":"Nature"},{"key":"7739_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25363-3","volume":"12","author":"P Plenge","year":"2021","unstructured":"Plenge, P. et al. The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter. Nat. Commun. 12, 5063 (2021).","journal-title":"Nat. Commun."},{"key":"7739_CR45","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/0006-8993(87)91355-2","volume":"404","author":"L Aniksztejn","year":"1987","unstructured":"Aniksztejn, L., Charton, G. & Ben-Ari, Y. Selective release of endogenous zinc from the hippocampal mossy fibers in situ. Brain Res. 404, 58\u201364 (1987).","journal-title":"Brain Res."},{"key":"7739_CR46","doi-asserted-by":"publisher","first-page":"e1002909","DOI":"10.1371\/journal.pcbi.1002909","volume":"9","author":"T Stockner","year":"2013","unstructured":"Stockner, T. et al. Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model. PLoS Comput. Biol. 9, e1002909 (2013).","journal-title":"PLoS Comput. Biol."},{"key":"7739_CR47","doi-asserted-by":"publisher","first-page":"36928","DOI":"10.1074\/jbc.274.52.36928","volume":"274","author":"CJ Loland","year":"1999","unstructured":"Loland, C. J., Norregaard, L. & Gether, U. Defining proximity relationships in the tertiary structure of the dopamine transporter. Identification of a conserved glutamic acid as a third coordinate in the endogenous Zn2+-binding site. J. Biol. Chem. 274, 36928\u201336934 (1999).","journal-title":"J. Biol. Chem."},{"key":"7739_CR48","doi-asserted-by":"publisher","first-page":"2574","DOI":"10.1038\/nprot.2014.173","volume":"9","author":"A Goehring","year":"2014","unstructured":"Goehring, A. et al. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies. Nat. Protoc. 9, 2574\u20132585 (2014).","journal-title":"Nat. Protoc."},{"key":"7739_CR49","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1002\/pro.519","volume":"19","author":"MH Kubala","year":"2010","unstructured":"Kubala, M. H., Kovtun, O., Alexandrov, K. & Collins, B. M. Structural and thermodynamic analysis of the GFP:GFP-nanobody complex. Protein Sci. 19, 2389\u20132401 (2010).","journal-title":"Protein Sci."},{"key":"7739_CR50","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1107\/S205225252000929X","volume":"7","author":"H Guo","year":"2020","unstructured":"Guo, H. et al. Electron-event representation data enable efficient cryoEM file storage with full preservation of spatial and temporal resolution. IUCrJ 7, 860\u2013869 (2020).","journal-title":"IUCrJ"},{"key":"7739_CR51","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nmeth.4169","volume":"14","author":"A Punjani","year":"2017","unstructured":"Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290\u2013296 (2017).","journal-title":"Nat. Methods"},{"key":"7739_CR52","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1038\/s41586-022-05168-0","volume":"609","author":"NJ Wright","year":"2022","unstructured":"Wright, N. J. et al. Methotrexate recognition by the human reduced folate carrier SLC19A1. Nature 609, 1056\u20131062 (2022).","journal-title":"Nature"},{"key":"7739_CR53","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.1038\/s41592-020-00990-8","volume":"17","author":"A Punjani","year":"2020","unstructured":"Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214\u20131221 (2020).","journal-title":"Nat. Methods"},{"key":"7739_CR54","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583\u2013589 (2021).","journal-title":"Nature"},{"key":"7739_CR55","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1002\/pro.3943","volume":"30","author":"EF Pettersen","year":"2021","unstructured":"Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70\u201382 (2021).","journal-title":"Protein Sci."},{"key":"7739_CR56","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1002\/pro.3791","volume":"29","author":"A Casanal","year":"2020","unstructured":"Casanal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo-microscopy and crystallographic data. Protein Sci. 29, 1069\u20131078 (2020).","journal-title":"Protein Sci."},{"key":"7739_CR57","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1107\/S2059798319011471","volume":"75","author":"D Liebschner","year":"2019","unstructured":"Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861\u2013877 (2019).","journal-title":"Acta Crystallogr. D"},{"key":"7739_CR58","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1107\/S2059798318006551","volume":"74","author":"PV Afonine","year":"2018","unstructured":"Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531\u2013544 (2018).","journal-title":"Acta Crystallogr. D"},{"key":"7739_CR59","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1107\/S0907444909042073","volume":"66","author":"VB Chen","year":"2010","unstructured":"Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12\u201321 (2010).","journal-title":"Acta Crystallogr. D"},{"key":"7739_CR60","doi-asserted-by":"publisher","first-page":"e4525","DOI":"10.1002\/pro.4525","volume":"32","author":"M Gucwa","year":"2023","unstructured":"Gucwa, M. et al. CMM-An enhanced platform for interactive validation of metal binding sites. Protein Sci. 32, e4525 (2023).","journal-title":"Protein Sci."},{"key":"7739_CR61","doi-asserted-by":"publisher","first-page":"1485","DOI":"10.1126\/science.1249410","volume":"343","author":"A Amunts","year":"2014","unstructured":"Amunts, A. et al. Structure of the yeast mitochondrial large ribosomal subunit. Science 343, 1485\u20131489 (2014).","journal-title":"Science"},{"key":"7739_CR62","doi-asserted-by":"publisher","first-page":"e44365","DOI":"10.7554\/eLife.44365","volume":"8","author":"C Alvadia","year":"2019","unstructured":"Alvadia, C. et al. Cryo-EM structures and functional characterization of the murine lipid scramblase TMEM16F. eLife 8, e44365 (2019).","journal-title":"eLife"},{"key":"7739_CR63","doi-asserted-by":"publisher","first-page":"W296","DOI":"10.1093\/nar\/gky427","volume":"46","author":"A Waterhouse","year":"2018","unstructured":"Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296\u2013W303 (2018).","journal-title":"Nucleic Acids Res."},{"key":"7739_CR64","doi-asserted-by":"publisher","first-page":"3603","DOI":"10.1073\/pnas.0609573104","volume":"104","author":"M Quick","year":"2007","unstructured":"Quick, M. & Javitch, J. A. Monitoring the function of membrane transport proteins in detergent-solubilized form. Proc. Natl Acad. Sci. USA 104, 3603\u20133608 (2007).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7739_CR65","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1002\/prot.10613","volume":"55","author":"MP Jacobson","year":"2004","unstructured":"Jacobson, M. P. et al. A hierarchical approach to all-atom protein loop prediction. Proteins 55, 351\u2013367 (2004).","journal-title":"Proteins"},{"key":"7739_CR66","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","volume":"27","author":"GM Sastry","year":"2013","unstructured":"Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R. & Sherman, W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aided Mol. Des. 27, 221\u2013234 (2013).","journal-title":"J. Comput. Aided Mol. Des."},{"key":"7739_CR67","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1016\/j.str.2009.09.010","volume":"17","author":"J Gumbart","year":"2009","unstructured":"Gumbart, J., Trabuco, L. G., Schreiner, E., Villa, E. & Schulten, K. Regulation of the protein-conducting channel by a bound ribosome. Structure 17, 1453\u20131464 (2009).","journal-title":"Structure"},{"key":"7739_CR68","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1002\/(SICI)1097-0134(199604)24:4<433::AID-PROT3>3.0.CO;2-F","volume":"24","author":"L Zhang","year":"1996","unstructured":"Zhang, L. & Hermans, J. Hydrophilicity of cavities in proteins. Proteins 24, 433\u2013438 (1996).","journal-title":"Proteins"},{"key":"7739_CR69","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33\u201338 (1996).","journal-title":"J. Mol. Graph."},{"key":"7739_CR70","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.20945","volume":"29","author":"S Jo","year":"2008","unstructured":"Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859\u20131865 (2008).","journal-title":"J. Comput. Chem."},{"key":"7739_CR71","doi-asserted-by":"publisher","first-page":"D370","DOI":"10.1093\/nar\/gkr703","volume":"40","author":"MA Lomize","year":"2012","unstructured":"Lomize, M. A., Pogozheva, I. D., Joo, H., Mosberg, H. I. & Lomize, A. L. OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 40, D370\u2013D376 (2012). (Database issue).","journal-title":"Nucleic Acids Res."},{"key":"7739_CR72","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1021\/acs.jctc.9b00591","volume":"16","author":"C Tian","year":"2020","unstructured":"Tian, C. et al. ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. J. Chem. Theory Comput. 16, 528\u2013552 (2020).","journal-title":"J. Chem. Theory Comput."},{"key":"7739_CR73","doi-asserted-by":"publisher","first-page":"1726","DOI":"10.1021\/acs.jctc.1c01217","volume":"18","author":"CJ Dickson","year":"2022","unstructured":"Dickson, C. J., Walker, R. C. & Gould, I. R. Lipid21: complex lipid membrane simulations with AMBER. J. Chem. Theory Comput. 18, 1726\u20131736 (2022).","journal-title":"J. Chem. Theory Comput."},{"key":"7739_CR74","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926\u2013935 (1983).","journal-title":"J. Chem. Phys."},{"key":"7739_CR75","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1021\/jp505875v","volume":"119","author":"P Li","year":"2015","unstructured":"Li, P., Song, L. F. & Merz, K. M. Jr Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J. Phys. Chem. B 119, 883\u2013895 (2015).","journal-title":"J. Phys. Chem. B"},{"key":"7739_CR76","doi-asserted-by":"publisher","first-page":"8432","DOI":"10.1039\/C7CP08185E","volume":"20","author":"J Yoo","year":"2018","unstructured":"Yoo, J. & Aksimentiev, A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Phys. Chem. Chem. Phys. 20, 8432\u20138449 (2018).","journal-title":"Phys. Chem. Chem. Phys."},{"key":"7739_CR77","doi-asserted-by":"publisher","first-page":"4291","DOI":"10.1021\/acs.jctc.1c00302","volume":"17","author":"C Lu","year":"2021","unstructured":"Lu, C. et al. OPLS4: improving force field accuracy on challenging regimes of chemical space. J. Chem. Theory Comput. 17, 4291\u20134300 (2021).","journal-title":"J. Chem. Theory Comput."},{"key":"7739_CR78","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s10822-007-9133-z","volume":"21","author":"JC Shelley","year":"2007","unstructured":"Shelley, J. C. et al. Epik: a software program for pKa prediction and protonation state generation for drug-like molecules. J. Comput. Aided Mol. Des. 21, 681\u2013691 (2007).","journal-title":"J. Comput. Aided Mol. Des."},{"key":"7739_CR79","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"J Wang","year":"2004","unstructured":"Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157\u20131174 (2004).","journal-title":"J. Comput. Chem."},{"key":"7739_CR80","doi-asserted-by":"publisher","first-page":"114502","DOI":"10.1063\/5.0019056","volume":"153","author":"X He","year":"2020","unstructured":"He, X., Man, V. H., Yang, W., Lee, T. S. & Wang, J. A fast and high-quality charge model for the next generation general AMBER force field. J. Chem. Phys. 153, 114502 (2020).","journal-title":"J. Chem. Phys."},{"key":"7739_CR81","unstructured":"Case, D. A. et al. AMBER 2020 (University of California, San Francisco, 2020)."},{"key":"7739_CR82","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.1080\/00268978800101881","volume":"65","author":"RW Pastor","year":"1988","unstructured":"Pastor, R. W., Brooks, B. R. & Szabo, A. An analysis of the accuracy of Langevin and molecular dynamics algorithms. Mol. Phys. 65, 1409\u20131419 (1988).","journal-title":"Mol. Phys."},{"key":"7739_CR83","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/j.cplett.2003.12.039","volume":"384","author":"J Aqvist","year":"2004","unstructured":"Aqvist, J., Wennerstrom, P., Nervall, M., Bjelic, S. & Brandsdal, B. O. Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm. Chem. Phys. Lett. 384, 288\u2013294 (2004).","journal-title":"Chem. Phys. Lett."},{"key":"7739_CR84","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089\u201310092 (1993).","journal-title":"J. Chem. Phys."},{"key":"7739_CR85","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"J-P Ryckaert","year":"1977","unstructured":"Ryckaert, J.-P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Physics 23, 327\u2013341 (1977).","journal-title":"J. Comput. Physics"},{"key":"7739_CR86","doi-asserted-by":"publisher","first-page":"6183","DOI":"10.1021\/acs.jcim.3c01153","volume":"63","author":"DA Case","year":"2023","unstructured":"Case, D. A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183\u20136191 (2023).","journal-title":"J. Chem. Inf. Model."},{"key":"7739_CR87","doi-asserted-by":"publisher","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"DR Roe","year":"2013","unstructured":"Roe, D. R. & Cheatham, T. E. 3rd PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084\u20133095 (2013).","journal-title":"J. Chem. Theory Comput."},{"key":"7739_CR88","doi-asserted-by":"publisher","unstructured":"Sk, M. F. & Tajkhorshid, E. Raw data for: Structure of the human dopamine transporter and mechanisms of allosteric inhibition. Zenodo https:\/\/doi.org\/10.5281\/zenodo.11391488 (2024).","DOI":"10.5281\/zenodo.11391488"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07739-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07739-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07739-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,15]],"date-time":"2024-08-15T07:09:48Z","timestamp":1723705788000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07739-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,7]]},"references-count":88,"journal-issue":{"issue":"8025","published-print":{"date-parts":[[2024,8,15]]}},"alternative-id":["7739"],"URL":"https:\/\/doi.org\/10.1038\/s41586-024-07739-9","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,7]]},"assertion":[{"value":"14 December 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}