9EUP: Sodium-dependent dopamine transporter

Inhibitor-free outward-open structure of Drosophila dopamine transporter. Determined by electron microscopy at 3.0 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 7,602
Mol. weight: 113.78 kDa
Ligands: 144, CLR, Y01
Released: 24 Jul 2024

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

Secondary structure: helices and β-sheets

9EUP contains 51 α-helices and 52 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: 40 helices, 8 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	104-107	4
α-helix	108-137	30
α-helix	144-146	3
β-strand	157-158	2	1
β-strand	162	1	2
β-strand	208	1	2
β-strand	209-210	2	1
α-helix	211-215	5
α-helix	216-220	5
α-helix	223-225	3
β-strand	235	1	3
α-helix	237-254	18
α-helix	258-268	11
α-helix	271-284	14
α-helix	289-297	9
α-helix	301-305	5
α-helix	307-321	15
α-helix	327-332	6
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	438-441	4
α-helix	444-459	16
β-strand	464	1	3
α-helix	467-477	11
α-helix	481-492	12
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	4
β-strand	550-551	2	4
α-helix	554-581	28
α-helix	586-594	9

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	11-12	2	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	58-60	3	7
β-strand	68-73	6	5
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	102-104	3
β-strand	108-109	2	7
β-strand	113-115	3	7
β-strand	116-117	2	6
α-helix	120-122	3
β-strand	123	1	8
β-strand	128-130	3	9
β-strand	141-151	11	9
β-strand	152	1	8
β-strand	157-160	4	10
β-strand	165	1	10
β-strand	169-171	3	9
α-helix	172-174	3
β-strand	175-177	3	9
β-strand	180-190	11	9
β-strand	200-205	6	10
β-strand	210-215	6	10

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	19-25	7	11
α-helix	28-30	3
β-strand	34-39	6	12
β-strand	46-50	5	12
β-strand	54-55	2	12
β-strand	63-68	6	11
β-strand	71-76	6	11
α-helix	81-83	3
β-strand	86-91	6	12
β-strand	99	1	12
β-strand	103-106	4	12
β-strand	112	1	13
β-strand	116-119	4	14
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	14
β-strand	141	1	13
β-strand	145-151	7	15
β-strand	154-156	3	15
β-strand	160-164	5	14
α-helix	165-168	4
β-strand	174-183	10	14
α-helix	184-189	6
β-strand	192-199	8	15
β-strand	202-211	10	15

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>9EUP_1 Sodium-dependent dopamine transporter (chains A)
MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIP
LFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASF
TNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALC
LLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFS
AIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFV
IFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSS
FGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYS
ILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGY
EPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQL
VPR

Sequence of entity 2 (H), FASTA

>9EUP_2 9D5 ANTIBODY, HEAVY CHAIN (chains H)
MNFGLRLVFLVLILKGVQCEVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSP
EKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEV
RQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Sequence of entity 3 (L), FASTA

>9EUP_3 9D5 ANTIBODY, LIGHT CHAIN (chains L)
MDFQVQIFSFLLISASVAMSRGENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQ
QKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLT
FGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQN
GVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
144	Tris-hydroxymethyl-methyl-ammonium	C4 H12 N O3	1
CLR	Cholesterol	C27 H46 O	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1

Water and common crystallization additives (NA, CL) 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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