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Yorodumi- PDB-4xp4: X-ray structure of Drosophila dopamine transporter in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xp4 | |||||||||
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Title | X-ray structure of Drosophila dopamine transporter in complex with cocaine | |||||||||
Components |
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Keywords | transport protein/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / membrane protein-tranport protein complex / transport protein-inhibitor complex | |||||||||
Function / homology | Function and homology information Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / dopamine:sodium symporter activity / norepinephrine transport / circadian sleep/wake cycle / response to odorant / cocaine binding / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / dopamine:sodium symporter activity / norepinephrine transport / circadian sleep/wake cycle / response to odorant / cocaine binding / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / neuron projection / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | |||||||||
Authors | Aravind, P. / 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 | 4xp4.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xp4.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xp4 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xp4 | HTTPS FTP |
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-Related structure data
Related structure data | 4xp1C 4xp5C 4xp6C 4xp9C 4xpaC 4xpbC 4xpfC 4xpgC 4xphC 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: 25840.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
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#3: Antibody | Mass: 25921.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 61147.762 Da / Num. of mol.: 1 / Mutation: V74A, L415A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, CG8380, Dmel_CG8380 / Cell line (production host): GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6 |
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#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 7 types, 20 molecules
#5: Chemical | ChemComp-Y01 / | ||||||||||
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#6: Chemical | #7: Chemical | ChemComp-CLR / | #8: Chemical | ChemComp-COC / | #9: Chemical | #10: Chemical | ChemComp-CL / | #11: 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: 5.33 Å3/Da / Density % sol: 76.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: PEG 400 (37%), NaMES (0.1M) |
-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: Sep 21, 2014 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.88 Å / Num. obs: 107985 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 76.72 Å2 |
Reflection shell | Resolution: 2.8→2.97 Å / Rmerge(I) obs: 1.805 / Mean I/σ(I) obs: 0.94 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Resolution: 2.8→45.88 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 72.78 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.88 Å
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LS refinement shell | Resolution: 2.8→2.83 Å
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