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- EMDB-38854: Cryo-EM structure of human dopamine transporter in complex with m... -

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Basic information

Entry
Database: EMDB / ID: EMD-38854
TitleCryo-EM structure of human dopamine transporter in complex with methylphenidate
Map data
Sample
  • Complex: human dopamine transporter in complex with methylphenidate
    • Protein or peptide: Sodium-dependent dopamine transporter
  • Ligand: methyl (2~{R})-2-phenyl-2-[(2~{R})-piperidin-2-yl]ethanoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
Keywordshuman dopamine transporter in complex with methylphenidate / 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 / 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
Sodium:neurotransmitter symporter, dopamine / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsZhao Y / Li Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nature / Year: 2024
Title: Dopamine reuptake and inhibitory mechanisms in human dopamine transporter
Authors: Zhao Y / Li Y
History
DepositionJan 25, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_38854.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.382
Minimum - Maximum-1.5313497 - 2.1122732
Average (Standard dev.)-0.0005797998 (±0.050462138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : human dopamine transporter in complex with methylphenidate

EntireName: human dopamine transporter in complex with methylphenidate
Components
  • Complex: human dopamine transporter in complex with methylphenidate
    • Protein or peptide: Sodium-dependent dopamine transporter
  • Ligand: methyl (2~{R})-2-phenyl-2-[(2~{R})-piperidin-2-yl]ethanoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION

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Supramolecule #1: human dopamine transporter in complex with methylphenidate

SupramoleculeName: human dopamine transporter in complex with methylphenidate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium-dependent dopamine transporter

MacromoleculeName: Sodium-dependent dopamine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.451426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: methyl (2~{R})-2-phenyl-2-[(2~{R})-piperidin-2-yl]ethanoate

MacromoleculeName: methyl (2~{R})-2-phenyl-2-[(2~{R})-piperidin-2-yl]ethanoate
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1D5U
Molecular weightTheoretical: 233.306 Da

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194911
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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