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Yorodumi- PDB-9eup: Inhibitor-free outward-open structure of Drosophila dopamine tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9eup | ||||||||||||||||||||||||||||||||||||
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Title | Inhibitor-free outward-open structure of Drosophila dopamine transporter | ||||||||||||||||||||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / SLC6A3 / Dopamine transporter / neurotransmitter sodium symporters | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / response to odorant / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / norepinephrine transport / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / response to odorant / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / norepinephrine transport / dopamine transport / sleep / dopamine uptake involved in synaptic transmission / amino acid transport / neuronal cell body membrane / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / axon / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Drosophila melanogaster (fruit fly) Mus musculus (house mouse) | ||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||||||||||||||||||||||||||
Authors | Pedersen, C.N. / Yang, F. / Ita, S. / Xu, Y. / Akunuri, R. / Trampari, S. / Neumann, C.M.T. / Desdorf, L.M. / Schioett, B. / Salvino, J.M. ...Pedersen, C.N. / Yang, F. / Ita, S. / Xu, Y. / Akunuri, R. / Trampari, S. / Neumann, C.M.T. / Desdorf, L.M. / Schioett, B. / Salvino, J.M. / Mortensen, O.V. / Nissen, P. / Shahsavar, A. | ||||||||||||||||||||||||||||||||||||
Funding support | Denmark, United States, 11items
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Citation | Journal: J Neurochem / Year: 2024 Title: Cryo-EM structure of the dopamine transporter with a novel atypical non-competitive inhibitor bound to the orthosteric site. Authors: Clara Nautrup Pedersen / Fuyu Yang / Samantha Ita / Yibin Xu / Ravikumar Akunuri / Sofia Trampari / Caroline Marie Teresa Neumann / Lasse Messell Desdorf / Birgit Schiøtt / Joseph M Salvino ...Authors: Clara Nautrup Pedersen / Fuyu Yang / Samantha Ita / Yibin Xu / Ravikumar Akunuri / Sofia Trampari / Caroline Marie Teresa Neumann / Lasse Messell Desdorf / Birgit Schiøtt / Joseph M Salvino / Ole Valente Mortensen / Poul Nissen / Azadeh Shahsavar / Abstract: The regulation of dopamine (DA) removal from the synaptic cleft is a crucial process in neurotransmission and is facilitated by the sodium- and chloride-coupled dopamine transporter DAT. ...The regulation of dopamine (DA) removal from the synaptic cleft is a crucial process in neurotransmission and is facilitated by the sodium- and chloride-coupled dopamine transporter DAT. Psychostimulant drugs, cocaine, and amphetamine, both block the uptake of DA, while amphetamine also triggers the release of DA. As a result, they prolong or even amplify neurotransmitter signaling. Atypical inhibitors of DAT lack cocaine-like rewarding effects and offer a promising strategy for the treatment of drug use disorders. Here, we present the 3.2 Å resolution cryo-electron microscopy structure of the Drosophila melanogaster dopamine transporter (dDAT) in complex with the atypical non-competitive inhibitor AC-4-248. The inhibitor partially binds at the central binding site, extending into the extracellular vestibule, and locks the transporter in an outward open conformation. Our findings propose mechanisms for the non-competitive inhibition of DAT and attenuation of cocaine potency by AC-4-248 and provide a basis for the rational design of more efficacious atypical inhibitors. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9eup.cif.gz | 366 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9eup.ent.gz | 297.3 KB | Display | PDB format |
PDBx/mmJSON format | 9eup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/9eup ftp://data.pdbj.org/pub/pdb/validation_reports/eu/9eup | HTTPS FTP |
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-Related structure data
Related structure data | 19979MC 9euoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60939.520 Da / Num. of mol.: 1 / Mutation: V74A, V275A, V311A, L415A, G538L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, fmn, CG8380 / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6 |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25921.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) |
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#3: Antibody | Mass: 25840.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) |
-Non-polymers , 5 types, 6 molecules
#4: Chemical | ChemComp-Y01 / | ||
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#5: Chemical | ChemComp-144 / | ||
#6: Chemical | ChemComp-CLR / | ||
#7: Chemical | #8: Chemical | ChemComp-CL / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Inhibitor-free Drosophila melanogaster dopamine transporter in complex with Fab 9D5 Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.107602 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Drosophila melanogaster (fruit fly) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 59.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4294 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137600 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4M48 Accession code: 4M48 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||
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