7TXT: Human serotonin transporter

Structure of human serotonin transporter bound to small molecule '8090 in lipid nanodisc and NaCl. Determined by electron microscopy at 3.0 Å resolution. Released 15 Mar 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 6,093
Mol. weight: 86.4 kDa
Ligands: KWC
Released: 15 Mar 2023

Explore 7TXT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TXT contains 50 α-helices and 31 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	1
α-helix	26	1
β-strand	29-31	3	2
β-strand	37-42	6	1
α-helix	48-50	3
β-strand	53-58	6	2
β-strand	64-71	8	2
β-strand	76-79	4	2
β-strand	84	1	1
β-strand	87-92	6	1
β-strand	97-102	6	1
α-helix	107-109	3
β-strand	111-116	6	2
β-strand	130	1	2
β-strand	134-138	5	2

Chain D: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	3
β-strand	30-33	4	4
β-strand	39-45	7	3
β-strand	51	1	5
β-strand	54	1	5
β-strand	57-62	6	4
β-strand	69-72	4	4
α-helix	77	1
β-strand	78	1	4
α-helix	79	1
β-strand	86-91	6	3
β-strand	94-99	6	3
α-helix	104-106	3
β-strand	108-114	7	4
α-helix	121	1
β-strand	122	1	4
α-helix	123	1
β-strand	126-130	5	4

Chain S: 42 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	85-96	12
α-helix	99	1
α-helix	100-104	5
α-helix	105-111	7
α-helix	114-117	4
α-helix	118-124	7
α-helix	125-129	5
α-helix	130-143	14
α-helix	149-152	4
α-helix	156-159	4
α-helix	160-189	30
β-strand	209	1	6
β-strand	225	1	6
α-helix	227-230	4
α-helix	231-236	6
α-helix	239-241	3
β-strand	251	1	7
α-helix	253-269	17
α-helix	274-284	11
α-helix	287-301	15
α-helix	305-313	9
α-helix	317-321	5
α-helix	323-337	15
α-helix	343-349	7
α-helix	357-389	33
α-helix	394-398	5
α-helix	405-409	5
α-helix	410-416	7
α-helix	420-453	34
α-helix	455-458	4
α-helix	462-477	16
α-helix	479-481	3
β-strand	482	1	7
α-helix	485-495	11
α-helix	499-510	12
α-helix	511-515	5
α-helix	518-529	12
α-helix	532-534	3
α-helix	535-539	5
α-helix	540-544	5
α-helix	545-557	13
β-strand	564-565	2	8
β-strand	568-569	2	8
α-helix	570-571	2
α-helix	572-586	15
α-helix	588-599	12
α-helix	604-612	9
α-helix	614-615	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
15B8 Fab heavy chain	C	protein	120	Mus musculus
15B8 Fab light chain	D	protein	111	Mus musculus
Sodium-dependent serotonin transporter	S	protein	541	Homo sapiens	P31645 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7TXT_1 15B8 Fab heavy chain (chains C)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVTVS

Sequence of entity 2 (D), FASTA

>7TXT_2 15B8 Fab light chain (chains D)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEIK

Sequence of entity 3 (S), FASTA

>7TXT_3 Sodium-dependent serotonin transporter (chains S)
GERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYME
LALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLP
WTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLA
LCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPN
WQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSG
FVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGL
DSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYA
TGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSF
LMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPET
P

Ligands and cofactors

ID	Name	Formula	Copies
KWC	1-[4-(4-fluorophenyl)-1,3-thiazol-2-yl]piperazine	C13 H14 F N3 S	1

Primary citation

Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Singh, I., Seth, A., Billesbolle, C.B. et al. Cell (2023) 186:2160-2175.e17. DOI 10.1016/j.cell.2023.04.010 · PubMed

Other PDB entries of the same protein (UniProt P31645 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HCO 2.78 Å, Outward-open structure of human serotonin transporter bound to vilazodone
5I6X 3.14 Å, X-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the…
5I71 3.15 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
9VWS 3.2 Å, Cryo-EM structure of human serotonin transporter in complex with tesofensine
5I73 3.24 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
9IY7 3.27 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with S-ketamine
6VRH 3.3 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine…
7LIA 3.3 Å, 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in…
5I74 3.4 Å, X-ray structure of the ts3 human serotonin transporter complexed with Br-citalopram at…
9PNS 3.4 Å, Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc…
5I75 3.49 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
7LI6 3.5 Å, apo SERT reconstituted in lipid nanodisc in KCl

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