6VRK: Wild-type human serotonin transporter

Cryo-EM structure of the wild-type human serotonin transporter complexed with Br-paroxetine and 8B6 Fab. Determined by electron microscopy at 4.1 Å resolution. Released 11 Mar 2020.

Method: Electron microscopy
Resolution: 4.1 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,141
Mol. weight: 119.12 kDa
Ligands: NAG, LMT, RFS
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6VRK contains 41 α-helices and 33 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: 37 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	85-96	12
α-helix	100-104	5
α-helix	105-111	7
β-strand	114	1	1
α-helix	115-117	3
α-helix	118-124	7
α-helix	125-129	5
α-helix	130-143	14
α-helix	149-153	5
α-helix	156-158	3
α-helix	160-189	30
α-helix	227-234	8
α-helix	239-241	3
β-strand	251	1	2
α-helix	253-270	18
α-helix	274-284	11
α-helix	287-299	13
α-helix	305-313	9
β-strand	315	1	1
α-helix	319-321	3
α-helix	323-337	15
α-helix	344-348	5
α-helix	357-389	33
α-helix	394-397	4
α-helix	404	1
α-helix	405-410	6
α-helix	411-415	5
α-helix	420-453	34
α-helix	466-477	12
β-strand	482	1	2
α-helix	485-494	10
α-helix	498-510	13
α-helix	511-515	5
α-helix	518-528	11
α-helix	535-539	5
α-helix	540-544	5
α-helix	545-556	12
β-strand	564-565	2	3
β-strand	568-569	2	3
α-helix	570-571	2
α-helix	572-583	12
α-helix	588-599	12
α-helix	604-612	9

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	10
β-strand	29-30	2	11
β-strand	37-38	2	12
β-strand	41	1	10
α-helix	48-50	3
β-strand	52-58	7	9
β-strand	64-68	5	9
β-strand	88-89	2	12
β-strand	92	1	13
α-helix	93-95	3
β-strand	97	1	13
β-strand	100-102	3	12
β-strand	112-118	7	9
β-strand	134-135	2	11

Chain C: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	4
β-strand	38-41	4	5
β-strand	43-45	3	4
β-strand	49	1	6
β-strand	53-58	6	7
β-strand	65-69	5	7
β-strand	73-74	2	7
α-helix	75	1
β-strand	87	1	8
β-strand	88	1	6
β-strand	90	1	8
β-strand	93-96	4	5
β-strand	105-110	6	7
α-helix	116	1
β-strand	117	1	9
β-strand	119	1	4
β-strand	122	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	630	Homo sapiens	P31645 (AlphaFold model)
8B6 antibody, light chain	C	protein	214	Mus musculus	A0A0U5BC76 (AlphaFold model)
8B6 antibody, heavy chain	B	protein	221	Mus musculus

Sequence of entity 1 (A), FASTA

>6VRK_1 Sodium-dependent serotonin transporter (chains A)
METTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYSAVPSPGAGDDTR
HSIPATTTTLVAELHQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLP
YTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIM
AWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIH
RSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGA
TLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQD
ALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPAS
TFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVT
LTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRIC
WVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIIT
PGTFKERIIKSITPETPTEIPCGDIRLNAV

Sequence of entity 2 (C), FASTA

>6VRK_2 8B6 antibody, light chain (chains C)
DIVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLIYSASYRYTGVPD
RFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSIPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (B), FASTA

>6VRK_3 8B6 antibody, heavy chain (chains B)
EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKQSHGKSLEWIGNINPNNGGTSY
NQKFKGKATLTVDKSSTTAYMELRSLTSEDSAVYYCTRSPVRPYYFDYWGQGTTLTVSSA
KTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGL
YTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	1
RFS	Br-paroxetine	C19 H20 Br N O3	1

Primary citation

Chemical and structural investigation of the paroxetine-human serotonin transporter complex. Coleman, J.A., Navratna, V., Antermite, D. et al. Elife (2020) 9. DOI 10.7554/eLife.56427 · 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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