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Yorodumi- PDB-4xph: X-ray structure of Drosophila dopamine transporter with subsiteB ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xph | |||||||||
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Title | X-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to 3,4dichlorophenethylamine | |||||||||
Components |
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Keywords | protein transport/inhibitor / integral membrane protein / neurotransmitter transporter / protein transport-inhibitor complex | |||||||||
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 / neuron projection / axon / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | |||||||||
Authors | Penmatsa, A. / Wang, K. / Gouaux, E. | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Neurotransmitter and psychostimulant recognition by the dopamine transporter. Authors: Wang, K.H. / Penmatsa, A. / Gouaux, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xph.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xph.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 4xph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xph ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xph | HTTPS FTP |
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-Related structure data
Related structure data | 4xp1C 4xp4C 4xp5C 4xp6C 4xp9C 4xpaC 4xpbC 4xpfC 4xpgC 4xptC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23320.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse) |
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#3: Antibody | Mass: 23619.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 59878.367 Da / Num. of mol.: 1 Mutation: V74A, L415A, D121G, S426M, DEL 162-202, DEL1-20, DEL603-631 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, CG8380 / Cell line (production host): HEK293s / Production host: Homo sapiens (human) / References: UniProt: Q9NB97, UniProt: Q7K4Y6*PLUS |
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#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose |
-Non-polymers , 6 types, 23 molecules
#5: Chemical | ChemComp-P4G / | ||||||
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#6: Chemical | ChemComp-42J / | ||||||
#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Chemical | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.5 Å3/Da / Density % sol: 77.62 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 400, 33%; NaMES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 52939 / % possible obs: 97.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 92.33 Å2 / Rmerge(I) obs: 0.074 / Χ2: 2.187 / Net I/av σ(I): 23.667 / Net I/σ(I): 12.4 / Num. measured all: 203265 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 2.9→48.106 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.75 Å2 / Biso mean: 92.0325 Å2 / Biso min: 60.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→48.106 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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