7LWD: Wild-type human serotonin transporter

Cryo-EM structure of the wild-type human serotonin transporter complexed with vilazodone, imipramine and 15B8 Fab. Determined by electron microscopy at 3.65 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 3.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,163
Mol. weight: 86.76 kDa
Ligands: IXX, YG7, NAG
Released: 11 Aug 2021

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

Secondary structure: helices and β-sheets

7LWD contains 41 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: 36 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	85-96	12
α-helix	100-104	5
α-helix	105-111	7
α-helix	118-128	11
α-helix	130-143	14
α-helix	151-154	4
α-helix	156-159	4
α-helix	160-188	29
α-helix	227-231	5
α-helix	232-236	5
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	281-284	4
α-helix	287-301	15
α-helix	306-312	7
α-helix	317-320	4
α-helix	323-337	15
α-helix	344-348	5
α-helix	361-389	29
α-helix	402-404	3
α-helix	405-409	5
α-helix	410-416	7
α-helix	425-453	29
α-helix	466-476	11
β-strand	482	1	2
α-helix	486-493	8
α-helix	499-510	12
α-helix	511-515	5
α-helix	518-529	12
α-helix	532-534	3
α-helix	535-543	9
α-helix	545-556	12
α-helix	560-561	2
β-strand	565	1	3
β-strand	568	1	3
α-helix	569-571	3
α-helix	573-584	12
α-helix	588-599	12
α-helix	604-610	7

Chain H: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	4
β-strand	25	1	5
β-strand	29	1	6
β-strand	38-42	5	5
β-strand	44	1	4
α-helix	48-50	3
β-strand	55-58	4	7
β-strand	66-69	4	7
β-strand	78-79	2	7
α-helix	83-86	4
β-strand	87-92	6	5
β-strand	97-102	6	5
α-helix	107-109	3
β-strand	112-114	3	7
β-strand	118	1	8
α-helix	121-123	3
β-strand	127	1	8
β-strand	136	1	6

Chain L: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	9
β-strand	30-31	2	10
β-strand	42-45	4	9
β-strand	50-51	2	11
β-strand	54-55	2	11
β-strand	57-61	5	12
β-strand	62	1	13
β-strand	69-73	5	12
β-strand	77-78	2	12
β-strand	86	1	14
β-strand	89-91	3	9
β-strand	94-96	3	9
β-strand	99	1	14
α-helix	100-101	2
β-strand	109	1	13
β-strand	112-114	3	12
β-strand	127-128	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	541	Homo sapiens	P31645 (AlphaFold model)
heavy chain antibody fragment	H	protein	118	Mus musculus
light chain antibody fragment	L	protein	110	Mus musculus

Sequence of entity 1 (A), FASTA

>7LWD_1 Sodium-dependent serotonin transporter (chains A)
GERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYME
LALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLP
WTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLA
LCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPN
WQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSG
FVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGL
DSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYA
TGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSF
LMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPET
P

Sequence of entity 2 (H), FASTA

>7LWD_2 heavy chain antibody fragment (chains H)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVT

Sequence of entity 3 (L), FASTA

>7LWD_3 light chain antibody fragment (chains L)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEI

Ligands and cofactors

ID	Name	Formula	Copies
IXX	3-(5H-dibenzo[b,f]azepin-5-yl)-n,n-dimethylpropan-1-amine	C19 H24 N2	1
YG7	5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide	C26 H27 N5 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter. Plenge, P., Yang, D., Salomon, K. et al. Nat Commun (2021) 12:5063-5063. DOI 10.1038/s41467-021-25363-3 · 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…

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