9EUO: Sodium-dependent dopamine transporter

Outward-open structure of Drosophila dopamine transporter bound to an atypical non-competitive inhibitor. Determined by electron microscopy at 3.2 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 6,059
Mol. weight: 114.09 kDa
Ligands: CLR, 144, Y01, A1H8F
Released: 24 Jul 2024

Explore 9EUO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EUO contains 46 α-helices and 28 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: 41 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	48-51	4
α-helix	53-59	7
α-helix	62-65	4
α-helix	66-72	7
α-helix	73-77	5
α-helix	78-91	14
α-helix	95-102	8
α-helix	104-106	3
α-helix	108-137	30
α-helix	144-146	3
β-strand	157-158	2	1
β-strand	209-210	2	1
α-helix	211-215	5
α-helix	216-221	6
α-helix	223-225	3
β-strand	235	1	2
α-helix	237-254	18
α-helix	258-268	11
α-helix	271-285	15
α-helix	289-297	9
α-helix	303-305	3
α-helix	307-321	15
α-helix	327-333	7
α-helix	341-369	29
α-helix	370-374	5
α-helix	378-381	4
α-helix	386-387	2
α-helix	388-392	5
α-helix	393-397	5
α-helix	403-436	34
α-helix	438-440	3
α-helix	444-462	19
β-strand	464	1	2
α-helix	467-477	11
α-helix	480-492	13
α-helix	493-499	7
α-helix	500-511	12
α-helix	514-516	3
α-helix	517-521	5
α-helix	522-526	5
α-helix	527-540	14
β-strand	546-547	2	3
β-strand	550-551	2	3
α-helix	554-568	15
α-helix	570-581	12
α-helix	586-594	9

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	35-39	5	8
β-strand	45-51	7	8
β-strand	58-60	3	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-97	6	8
β-strand	109	1	8
β-strand	113-117	5	8

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	11-13	3	5
β-strand	19-29	11	4
β-strand	34-39	6	6
β-strand	46-49	4	6
α-helix	54	1
β-strand	55	1	6
α-helix	56	1
β-strand	63-76	14	4
β-strand	86-91	6	6
α-helix	97	1
β-strand	98-99	2	6
β-strand	103-104	2	6
β-strand	105-107	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent dopamine transporter	A	protein	543	Drosophila melanogaster	Q7K4Y6 (AlphaFold model)
9D5 antibody, light chain	L	protein	237	Mus musculus
9D5 antibody, heavy chain	H	protein	240	Mus musculus

Sequence of entity 1 (A), FASTA

>9EUO_1 Sodium-dependent dopamine transporter (chains A)
MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIP
LFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASF
TNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALC
LLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFS
AIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFV
IFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSS
FGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYS
ILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGY
EPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQL
VPR

Sequence of entity 2 (L), FASTA

>9EUO_2 9D5 ANTIBODY, LIGHT CHAIN (chains L)
MDFQVQIFSFLLISASVAMSRGENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQ
QKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLT
FGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQN
GVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>9EUO_3 9D5 ANTIBODY, HEAVY CHAIN (chains H)
MNFGLRLVFLVLILKGVQCEVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSP
EKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEV
RQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
144	Tris-hydroxymethyl-methyl-ammonium	C4 H12 N O3	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1
A1H8F	N-[3-(6-chloranyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-2-yl)propyl]butanamide	C18 H24 Cl N3 O	1

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

Primary citation

Cryo-EM structure of the dopamine transporter with a novel atypical non-competitive inhibitor bound to the orthosteric site. Pedersen, C.N., Yang, F., Ita, S. et al. J Neurochem (2024) 168:2043-2055. DOI 10.1111/jnc.16179 · PubMed

Other PDB entries of the same protein (UniProt Q7K4Y6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WGT 2.75 Å, X-ray structure of thermostabilized Drosophila dopamine transporter with GABA…
4XP4 2.8 Å, X-ray structure of Drosophila dopamine transporter in complex with cocaine
4XP9 2.8 Å, X-ray structure of Drosophila dopamine transporter bound to psychostimulant D-amphetamine
6M2R 2.8 Å, X-ray structure of a functional Drosophila dopamine transporter in L-norepinephrine…
6M0Z 2.88 Å, X-ray structure of Drosophila dopamine transporter with NET-like mutations…
4XP1 2.89 Å, X-ray structure of Drosophila dopamine transporter bound to neurotransmitter dopamine
4XPH 2.9 Å, X-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M)…
7WLW 2.9 Å, X-ray structure of thermostabilized Drosophila dopamine transporter with GABA…
4XPA 2.95 Å, X-ray structure of Drosophila dopamine transporter bound to 3,4dichlorophenethylamine
4M48 2.96 Å, X-ray structure of dopamine transporter elucidates antidepressant mechanism
4XNU 2.98 Å, X-ray structure of Drosophila dopamine transporter in complex with nisoxetine
4XNX 3.0 Å, X-ray structure of Drosophila dopamine transporter in complex with reboxetine

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