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Yorodumi- EMDB-43128: Structure of the human dopamine transporter in complex with beta-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43128 | |||||||||
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Title | Structure of the human dopamine transporter in complex with beta-CFT, MRS7292 and divalent zinc | |||||||||
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Sample |
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Keywords | Transport / Membrane / Inhibitor / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Dopamine clearance from the synaptic cleft / amine binding / adenohypophysis development / dopamine uptake / hyaloid vascular plexus regression / dopamine binding / norepinephrine:sodium symporter activity / dopamine:sodium symporter activity ...Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Dopamine clearance from the synaptic cleft / amine binding / adenohypophysis development / dopamine uptake / hyaloid vascular plexus regression / dopamine binding / norepinephrine:sodium symporter activity / dopamine:sodium symporter activity / norepinephrine transport / regulation of dopamine metabolic process / neurotransmitter transmembrane transporter activity / dopamine transport / dopaminergic synapse / flotillin complex / dopamine catabolic process / monoamine transmembrane transporter activity / monoamine transport / Na+/Cl- dependent neurotransmitter transporters / positive regulation of multicellular organism growth / response to iron ion / neurotransmitter transport / dopamine biosynthetic process / amino acid transport / heterocyclic compound binding / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / sodium ion transmembrane transport / prepulse inhibition / axon terminus / response to cAMP / lactation / protein phosphatase 2A binding / response to cocaine / cognition / locomotory behavior / response to nicotine / sensory perception of smell / presynaptic membrane / protease binding / postsynaptic membrane / response to ethanol / neuron projection / response to xenobiotic stimulus / membrane raft / axon / signaling receptor binding / neuronal cell body / protein-containing complex binding / cell surface / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||
Authors | Srivastava DK / Gouaux E | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2024 Title: Structure of the human dopamine transporter and mechanisms of inhibition. Authors: Dushyant Kumar Srivastava / Vikas Navratna / Dilip K Tosh / Audrey Chinn / Md Fulbabu Sk / Emad Tajkhorshid / Kenneth A Jacobson / Eric Gouaux / Abstract: The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement. Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, ...The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement. Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, the human dopamine transporter (hDAT) and mechanisms by which it is inhibited by small molecules and Zn are without a high-resolution structural context. Here we determine the structure of hDAT in a tripartite complex with the competitive inhibitor and cocaine analogue, (-)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane (β-CFT), the non-competitive inhibitor MRS7292 and Zn (ref. ). We show how β-CFT occupies the central site, approximately halfway across the membrane, stabilizing the transporter in an outward-open conformation. MRS7292 binds to a structurally uncharacterized allosteric site, adjacent to the extracellular vestibule, sequestered underneath the extracellular loop 4 (EL4) and adjacent to transmembrane helix 1b (TM1b), acting as a wedge, precluding movement of TM1b and closure of the extracellular gate. A Zn ion further stabilizes the outward-facing conformation by coupling EL4 to EL2, TM7 and TM8, thus providing specific insights into how Zn restrains the movement of EL4 relative to EL2 and inhibits transport activity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43128.map.gz | 203.7 MB | EMDB map data format | |
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Header (meta data) | emd-43128-v30.xml emd-43128.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43128_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_43128.png | 72.4 KB | ||
Masks | emd_43128_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-43128.cif.gz | 6.9 KB | ||
Others | emd_43128_half_map_1.map.gz emd_43128_half_map_2.map.gz | 200.5 MB 200.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43128 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43128 | HTTPS FTP |
-Validation report
Summary document | emd_43128_validation.pdf.gz | 973.1 KB | Display | EMDB validaton report |
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Full document | emd_43128_full_validation.pdf.gz | 972.6 KB | Display | |
Data in XML | emd_43128_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_43128_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43128 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43128 | HTTPS FTP |
-Related structure data
Related structure data | 8vbyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43128.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.743 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43128_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43128_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43128_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Sodium dependent dopamine transporter in complex with inhibitor
+Supramolecule #1: Sodium dependent dopamine transporter in complex with inhibitor
+Macromolecule #1: Sodium-dependent dopamine transporter
+Macromolecule #2: methyl (1R,2S,3S,5S)-3-(4-fluorophenyl)-8-methyl-8-azabicyclo[3.2...
+Macromolecule #3: methyl (1S,2R,3S,4R,5R)-4-{2-[(5-chlorothiophen-2-yl)ethynyl]-6-(...
+Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #5: CHOLESTEROL HEMISUCCINATE
+Macromolecule #6: DECANE
+Macromolecule #7: PENTANE
+Macromolecule #8: HEPTANE
+Macromolecule #9: ZINC ION
+Macromolecule #10: SODIUM ION
+Macromolecule #11: DODECANE
+Macromolecule #12: PENTADECANE
+Macromolecule #13: N-OCTANE
+Macromolecule #14: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.0 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | monodisperse sample |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 6 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |