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- EMDB-38854: Cryo-EM structure of human dopamine transporter in complex with m... -
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Open data
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Basic information
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Title | Cryo-EM structure of human dopamine transporter in complex with methylphenidate | |||||||||
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![]() | human dopamine transporter in complex with methylphenidate / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 / dopaminergic synapse / neurotransmitter transmembrane transporter activity / dopamine transport / flotillin complex / monoamine transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / monoamine transport / dopamine catabolic process / positive regulation of multicellular organism growth / neurotransmitter transport / response to iron ion / dopamine biosynthetic process / dopamine uptake involved in synaptic transmission / amino acid transport / heterocyclic compound binding / neuronal cell body membrane / sodium ion transmembrane transport / prepulse inhibition / axon terminus / response to cAMP / lactation / protein phosphatase 2A binding / response to cocaine / locomotory behavior / response to nicotine / cognition / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
![]() | Zhao Y / Li Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Dopamine reuptake and inhibitory mechanisms in human dopamine transporter Authors: Zhao Y / Li Y | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | |||
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Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8y2gMC ![]() 38850 ![]() 38851 ![]() 38852 ![]() 38853 ![]() 8y2cC ![]() 8y2dC ![]() 8y2eC ![]() 8y2fC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : human dopamine transporter in complex with methylphenidate
Entire | Name: human dopamine transporter in complex with methylphenidate |
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Components |
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-Supramolecule #1: human dopamine transporter in complex with methylphenidate
Supramolecule | Name: human dopamine transporter in complex with methylphenidate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Sodium-dependent dopamine transporter
Macromolecule | Name: Sodium-dependent dopamine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 62.451426 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DRETWGKKVD FLLSVIGFAV DLANVWRFPY LCYKNGGGAF LVPYLLFMVI AGMPLFYMEL ALGQFNREGA AGVWKICPIL KGVGFTVIL ISLYVGFFYN VIIAWALHYL FSSFTTELPW IHCNNSWNSP NCSDAHPGDS SGDSSGLNDT FGTTPAAEYF E RGVLHLHQ ...String: DRETWGKKVD FLLSVIGFAV DLANVWRFPY LCYKNGGGAF LVPYLLFMVI AGMPLFYMEL ALGQFNREGA AGVWKICPIL KGVGFTVIL ISLYVGFFYN VIIAWALHYL FSSFTTELPW IHCNNSWNSP NCSDAHPGDS SGDSSGLNDT FGTTPAAEYF E RGVLHLHQ SHGIDDLGPP RWQLTACLVL VIVLLYFSLW KGVKTSGKVV WITATMPYVV LTALLLRGVT LPGAIDGIRA YL SVDFYRL CEASVWIDAA TQVCFSLGVG FGVLIAFSSY NKFTNNCYRD AIVTTSINSL TSFSSGFVVF SFLGYMAQKH SVP IGDVAK DGPGLIFIIY PEAIATLPLS SAWAVVFFIM LLTLGIDSAM GGMESVITGL IDEFQLLHRH RELFTLFIVL ATFL LSLFC VTNGGIYVFT LLDHFAAGTS ILFGVLIEAI GVAWFYGVGQ FSDDIQQMTG QRPSLYWRLC WKLVSPCFLL FVVVV SIVT FRPPHYGAYI FPDWANALGW VIATSSMAMV PIYAAYKFCS LPGSFREKLA YAIAPEKDRE LVDRGEVRQF TLRHWL KV UniProtKB: Sodium-dependent dopamine transporter |
-Macromolecule #2: methyl (2~{R})-2-phenyl-2-[(2~{R})-piperidin-2-yl]ethanoate
Macromolecule | Name: methyl (2~{R})-2-phenyl-2-[(2~{R})-piperidin-2-yl]ethanoate type: ligand / ID: 2 / Number of copies: 1 / Formula: A1D5U |
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Molecular weight | Theoretical: 233.306 Da |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #4: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #5: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 5 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194911 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |