6DZZ: Wild-type human serotonin transporter

Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation. Determined by electron microscopy at 3.6 Å resolution. Released 24 Apr 2019.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,141
Mol. weight: 87.01 kDa
Ligands: LMT, HJM
Released: 24 Apr 2019

Explore 6DZZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DZZ contains 43 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 A: 39 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	82-96	15
α-helix	100-104	5
α-helix	105-111	7
α-helix	118-124	7
α-helix	125-129	5
α-helix	130-143	14
α-helix	151-153	3
α-helix	160-175	16
α-helix	177-188	12
β-strand	207	1	1
β-strand	209	1	2
α-helix	218-220	3
β-strand	225	1	2
α-helix	227-231	5
α-helix	232-236	5
β-strand	251	1	3
α-helix	253-267	15
α-helix	280-281	2
α-helix	282-286	5
α-helix	287-292	6
α-helix	295-301	7
α-helix	311-313	3
α-helix	326-336	11
α-helix	344-350	7
α-helix	357-389	33
α-helix	406-415	10
α-helix	420-440	21
α-helix	444-447	4
α-helix	449-452	4
α-helix	465-475	11
β-strand	482	1	3
α-helix	486-489	4
α-helix	491-494	4
α-helix	499-510	12
α-helix	511-515	5
α-helix	518-528	11
α-helix	532-534	3
α-helix	535-538	4
α-helix	540-544	5
α-helix	545-558	14
α-helix	573-582	10
α-helix	588-595	8
α-helix	604-612	9
α-helix	614-615	2

Chain B: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	4
β-strand	29	1	5
β-strand	39-43	5	4
α-helix	48-50	3
β-strand	53-58	6	6
β-strand	65-71	7	6
β-strand	76-79	4	6
β-strand	87-92	6	4
β-strand	97-102	6	4
β-strand	112-117	6	6
β-strand	118	1	7
β-strand	121	1	1
β-strand	126	1	7
β-strand	134-135	2	6
β-strand	136	1	5

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	8
β-strand	30-31	2	9
β-strand	43	1	8
β-strand	58-62	5	10
α-helix	67-68	2
β-strand	69-73	5	10
β-strand	77-78	2	10
α-helix	79	1
β-strand	87-90	4	11
β-strand	95-98	4	11
α-helix	104-106	3
β-strand	109-113	5	10
β-strand	122	1	10
β-strand	126	1	10
β-strand	127-128	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	540	Homo sapiens	P31645 (AlphaFold model)
15B8 antibody heavy chain	B	protein	118	Mus musculus
15B8 antibody light chain	C	protein	110	Mus musculus

Sequence of entity 1 (A), FASTA

>6DZZ_1 Sodium-dependent serotonin transporter (chains A)
ERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMEL
ALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPW
TSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLAL
CIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNW
QKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGF
VIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLD
STFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYAT
GPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFL
MSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP

Sequence of entity 2 (B), FASTA

>6DZZ_2 15B8 antibody heavy chain (chains B)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVT

Sequence of entity 3 (C), FASTA

>6DZZ_3 15B8 antibody light chain (chains C)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEI

Ligands and cofactors

ID	Name	Formula	Copies
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	1
HJM	(5beta)-12-methoxyibogamine	C20 H26 N2 O	1

Primary citation

Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. Coleman, J.A., Yang, D., Zhao, Z. et al. Nature (2019) 569:141-145. DOI 10.1038/s41586-019-1135-1 · 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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