4M48: Transporter

X-ray structure of dopamine transporter elucidates antidepressant mechanism. Determined by X-ray diffraction at 2.96 Å resolution. Released 18 Sept 2013.

Method: X-ray diffraction
Resolution: 2.96 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 7,496
Mol. weight: 113.43 kDa
Ligands: CLR, 21B
Released: 18 Sept 2013

Explore 4M48 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4M48 contains 52 α-helices and 46 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, 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	108-123	16
α-helix	125-137	13
β-strand	157-158	2	1
β-strand	209-210	2	1
α-helix	211-214	4
α-helix	215-221	7
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	301-305	5
α-helix	307-321	15
α-helix	327-333	7
α-helix	341-373	33
α-helix	378-381	4
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	444-459	16
β-strand	464	1	2
α-helix	467-477	11
α-helix	482-492	11
α-helix	493-497	5
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	570-579	10
α-helix	586-594	9

Chain H: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-40	7	11
β-strand	44-51	8	11
β-strand	58-60	3	11
β-strand	69-73	5	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	108-109	2	11
β-strand	113-115	3	11
β-strand	116-117	2	10
β-strand	126-130	5	12
β-strand	141-151	11	12
β-strand	157-160	4	13
α-helix	161-163	3
β-strand	169-176	8	12
β-strand	181-190	10	12
α-helix	193-196	4
β-strand	200-205	6	13
α-helix	206-208	3
β-strand	210-215	6	13

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-29	11	4
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
α-helix	56	1
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	100	1	4
β-strand	103-107	5	5
β-strand	112	1	6
β-strand	115-119	5	7
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	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	174-183	10	7
α-helix	184-188	5
β-strand	192-198	7	8
α-helix	205	1
β-strand	206-211	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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

>4M48_1 Transporter (chains A)
MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIP
LFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASF
TNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALC
LLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFS
AIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFV
IFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSS
FGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYS
ILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGY
EPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQL
VPR

Sequence of entity 2 (L), FASTA

>4M48_2 9D5 antibody, light chain (chains L)
MDFQVQIFSFLLISASVAMSRGENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQ
QKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLT
FGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQN
GVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (H), FASTA

>4M48_3 9D5 antibody, heavy chain (chains H)
MNFGLRLVFLVLILKGVQCEVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSP
EKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEV
RQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
21B	Nortriptyline	C19 H21 N	1

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

Primary citation

X-ray structure of dopamine transporter elucidates antidepressant mechanism. Penmatsa, A., Wang, K.H., Gouaux, E. Nature (2013) 503:85-90. DOI 10.1038/nature12533 · 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
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
9EUP 3.0 Å, Inhibitor-free outward-open structure of Drosophila dopamine transporter

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4M48 is part of these collections:

Neurotransmission and the synapse

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