7LIA: Sodium-dependent serotonin transporter

5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation. Determined by electron microscopy at 3.3 Å resolution. Released 15 Dec 2021.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,279
Mol. weight: 88.96 kDa
Ligands: HP6, D10, SRO, CLR
Released: 15 Dec 2021

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

Secondary structure: helices and β-sheets

7LIA contains 38 α-helices and 30 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	85-96	12
α-helix	100-111	12
α-helix	115-117	3
α-helix	118-128	11
α-helix	130-143	14
α-helix	151-154	4
α-helix	156-158	3
α-helix	161-189	29
α-helix	227-230	4
α-helix	231-236	6
α-helix	239-241	3
β-strand	244	1	1
β-strand	247	1	1
β-strand	251	1	2
α-helix	253-269	17
α-helix	274-284	11
α-helix	287-299	13
α-helix	305-312	8
α-helix	319-321	3
α-helix	324-337	14
α-helix	344-349	6
α-helix	357-390	34
α-helix	404-405	2
α-helix	406-410	5
α-helix	411-416	6
α-helix	420-453	34
α-helix	455-457	3
α-helix	462-477	16
β-strand	482	1	2
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	535-557	23
β-strand	564-565	2	3
β-strand	568-569	2	3
α-helix	572-586	15
α-helix	588-599	12
α-helix	604-612	9
α-helix	614-616	3

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	4
β-strand	37-44	8	4
α-helix	48-50	3
β-strand	53-58	6	5
β-strand	64-71	8	5
β-strand	76-79	4	5
α-helix	82-84	3
β-strand	87-92	6	4
β-strand	97-102	6	4
α-helix	107-109	3
β-strand	112-118	7	5
β-strand	127-129	3	5
β-strand	134-135	2	5

Chain C: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	6
β-strand	30-32	3	7
β-strand	39-45	7	6
β-strand	50	1	8
β-strand	55	1	8
β-strand	57-62	6	7
β-strand	69-73	5	7
β-strand	77-78	2	7
β-strand	86-91	6	6
β-strand	94-99	6	6
β-strand	109-114	6	7
β-strand	116	1	9
β-strand	119	1	9
β-strand	126-129	4	7

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

>7LIA_1 Sodium-dependent serotonin transporter (chains A)
RETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELA
LGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWT
SCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALC
IMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQ
KLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFV
IFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDS
TFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATG
PAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLM
SPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP

Sequence of entity 2 (B), FASTA

>7LIA_2 variable domain of 15B8 antibody Fab heavy chain (chains B)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVT

Sequence of entity 3 (C), FASTA

>7LIA_3 variable domain of 15B8 antibody Fab light chain (chains C)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEI

Ligands and cofactors

ID	Name	Formula	Copies
HP6	Heptane	C7 H16	13
D10	Decane	C10 H22	5
SRO	Serotonin	C10 H12 N2 O	2
CLR	Cholesterol	C27 H46 O	1
LNK	Pentane	C5 H12	1

Water and common crystallization additives (NA, CL) are not listed.

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…
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

Browse structure collections

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