7LI8: Sodium-dependent serotonin transporter

apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in inward open conformation. Determined by electron microscopy at 3.9 Å resolution. Released 15 Dec 2021.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,181
Mol. weight: 87.61 kDa
Ligands: LNK, HP6, D12, D10
Released: 15 Dec 2021

Explore 7LI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LI8 contains 37 α-helices and 36 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 A: 35 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	84-90	7
α-helix	99-102	4
α-helix	104-111	8
α-helix	118-128	11
α-helix	130-142	13
α-helix	149-152	4
α-helix	160-175	16
α-helix	177-189	13
β-strand	209	1	1
α-helix	219-221	3
β-strand	225	1	1
α-helix	227-231	5
α-helix	232-236	5
β-strand	244	1	2
β-strand	247	1	2
β-strand	251	1	3
α-helix	253-267	15
α-helix	280-285	6
α-helix	288-300	13
α-helix	306-312	7
α-helix	317-319	3
α-helix	326-337	12
α-helix	344-348	5
α-helix	360-388	29
α-helix	394-396	3
α-helix	404-414	11
α-helix	420-447	28
α-helix	466-476	11
α-helix	479-481	3
β-strand	482	1	3
α-helix	486-495	10
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	4
β-strand	568-569	2	4
α-helix	572-584	13
α-helix	588-597	10
α-helix	604-612	9

Chain B: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	5
β-strand	29	1	6
β-strand	38-44	7	5
α-helix	48-50	3
β-strand	53-58	6	7
β-strand	64-70	7	7
β-strand	77-79	3	7
β-strand	87	1	8
β-strand	90-92	3	5
β-strand	97-101	5	5
β-strand	102	1	8
β-strand	112-113	2	7
β-strand	116-117	2	7
β-strand	118	1	9
β-strand	126	1	9
β-strand	136	1	6

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	10
β-strand	30-31	2	11
β-strand	43	1	10
β-strand	57-62	6	12
β-strand	69-73	5	12
β-strand	77-78	2	12
β-strand	87-90	4	13
β-strand	95-98	4	13
α-helix	104-106	3
β-strand	109-110	2	12
β-strand	113-114	2	12
β-strand	121	1	12
β-strand	126	1	12
β-strand	127-128	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	539	Homo sapiens	P31645 (AlphaFold model)
variable domain of 15B8 antibody Fab heavy chain	B	protein	118	Mus musculus
variable domain of 15B8 antibody Fab light chain	C	protein	110	Mus musculus

Sequence of entity 1 (A), FASTA

>7LI8_1 Sodium-dependent serotonin transporter (chains A)
RETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELA
LGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWT
SCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALC
IMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQ
KLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFV
IFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDS
TFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATG
PAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLM
SPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP

Sequence of entity 2 (B), FASTA

>7LI8_2 variable domain of 15B8 antibody Fab heavy chain (chains B)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVT

Sequence of entity 3 (C), FASTA

>7LI8_3 variable domain of 15B8 antibody Fab light chain (chains C)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEI

Ligands and cofactors

ID	Name	Formula	Copies
LNK	Pentane	C5 H12	1
HP6	Heptane	C7 H16	6
D12	Dodecane	C12 H26	3
D10	Decane	C10 H22	1
R16	Hexadecane	C16 H34	1

Primary citation

Illumination of serotonin transporter mechanism and role of the allosteric site. Yang, D., Gouaux, E. Sci Adv (2021) 7:eabl3857-eabl3857. DOI 10.1126/sciadv.abl3857 · 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
7TXT 3.0 Å, Structure of human serotonin transporter bound to small molecule '8090 in lipid nanodisc…
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…

Browse structure collections

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