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Yorodumi- PDB-8y2f: Cryo-EM structure of human dopamine transporter in complex with G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8y2f | ||||||
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Title | Cryo-EM structure of human dopamine transporter in complex with GBR12909 | ||||||
Components | Sodium-dependent dopamine transporter | ||||||
Keywords | MEMBRANE PROTEIN / human dopamine transporter human dopamine transporter | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
Authors | Zhao, Y. / Li, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2024 Title: Dopamine reuptake and inhibitory mechanisms in human dopamine transporter Authors: Zhao, Y. / Li, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8y2f.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8y2f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8y2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8y2f_validation.pdf.gz | 496.7 KB | Display | wwPDB validaton report |
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Full document | 8y2f_full_validation.pdf.gz | 499.9 KB | Display | |
Data in XML | 8y2f_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 8y2f_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/8y2f ftp://data.pdbj.org/pub/pdb/validation_reports/y2/8y2f | HTTPS FTP |
-Related structure data
Related structure data | 38853MC 8y2cC 8y2dC 8y2eC 8y2gC 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
#1: Protein | Mass: 61590.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A3, DAT1 / Production host: Homo sapiens (human) / References: UniProt: Q01959 | ||
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#2: Chemical | ChemComp-A1D5S / Mass: 450.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32F2N2O / Feature type: SUBJECT OF INVESTIGATION | ||
#3: Sugar | Has ligand of interest | Y | |
-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: human dopamine transporter in complex with GBR12909 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182906 / Symmetry type: POINT | ||||||||||||||||||||||||
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