7WGD: Sodium-dependent dopamine transporter

X-ray structure of thermostabilized Drosophila dopamine transporter with GABA transporter1-like substitutions in the binding site, in substrate-free form. Determined by X-ray diffraction at 3.2 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 7,574
Mol. weight: 108.03 kDa
Ligands: CLR, Y01
Released: 29 Jun 2022

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

Secondary structure: helices and β-sheets

7WGD contains 58 α-helices and 49 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: 43 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	47-49	3
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	108-120	13
α-helix	126-136	11
α-helix	144-146	3
β-strand	158	1	1
β-strand	210	1	1
α-helix	211-215	5
α-helix	216-220	5
α-helix	223-225	3
β-strand	235	1	2
α-helix	237-251	15
α-helix	258-268	11
α-helix	271-283	13
α-helix	289-297	9
α-helix	303-305	3
α-helix	307-320	14
α-helix	327-333	7
α-helix	341-373	33
α-helix	378-380	3
α-helix	386-387	2
α-helix	388-392	5
α-helix	393-397	5
α-helix	403-434	32
α-helix	438-441	4
α-helix	444-458	15
α-helix	459-463	5
β-strand	464	1	2
α-helix	467-475	9
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	552-553	2
α-helix	554-568	15
α-helix	570-579	10
α-helix	587-593	7

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	65	1	9
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
α-helix	102-104	3
β-strand	109	1	10
β-strand	113-117	5	10
α-helix	120-122	3
β-strand	123	1	11
β-strand	126-130	5	12
α-helix	131-132	2
β-strand	142-151	10	12
β-strand	152	1	11
β-strand	157-160	4	13
α-helix	161-163	3
β-strand	165	1	13
β-strand	169-171	3	12
α-helix	172-174	3
β-strand	175-176	2	12
β-strand	181-189	9	12
β-strand	199-205	7	13
α-helix	206-208	3
β-strand	210-216	7	13

Chain L: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-29	11	4
α-helix	31-33	3
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
β-strand	63-76	14	4
α-helix	81-83	3
β-strand	86-91	6	5
α-helix	97	1
β-strand	98-99	2	5
β-strand	103-107	5	5
β-strand	112	1	6
β-strand	115-119	5	7
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	7
β-strand	141	1	6
β-strand	146-151	6	8
β-strand	154-156	3	8
β-strand	160-164	5	7
α-helix	165-168	4
β-strand	174-182	9	7
α-helix	184-187	4
β-strand	192-198	7	8
β-strand	206-211	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent dopamine transporter	A	protein	536	Drosophila melanogaster	Q7K4Y6 (AlphaFold model)
Antibody fragment (9D5) Light Chain	L	protein	214	Mus musculus
Antibody fragment (9D5) heavy chain	H	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>7WGD_1 Sodium-dependent dopamine transporter (chains A)
DERETWSGKVDFLLSVIGYAVGLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYME
LALGQHNRKGAITCWGRLVPLFKGIGYAVVLISFYLNFYYNVIIAWSLRFFFASFTNSLP
WTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLI
VYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIY
KAEVWADAATQVFFSLGPGLGSLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFS
VLGYMAHTLGVRIEDVATSGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSQFGT
VEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILV
AVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPL
TYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQ

Sequence of entity 2 (L), FASTA

>7WGD_2 Antibody fragment (9D5) Light Chain (chains L)
ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVP
ARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (H), FASTA

>7WGD_3 Antibody fragment (9D5) heavy chain (chains H)
EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYY
SDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1

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

Primary citation

Structural insights into GABA transport inhibition using an engineered neurotransmitter transporter. Joseph, D., Nayak, S.R., Penmatsa, A. EMBO J (2022) 41:e110735-e110735. DOI 10.15252/embj.2022110735 · 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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