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Yorodumi- PDB-4xpt: X-ray structure of Drosophila dopamine transporter with subsiteB ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xpt | |||||||||
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Title | X-ray structure of Drosophila dopamine transporter with subsiteB mutations D121G/S426M and EL2 deletion of 162-201 in complex with substrate analogue 3,4 dichlorophen ethylamine | |||||||||
Components |
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Keywords | protein transport/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / transport protein-inhibitor complex / 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 / axon / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 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 | 4xpt.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xpt.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xpt_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4xpt_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4xpt_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 4xpt_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xpt ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xpt | HTTPS FTP |
-Related structure data
Related structure data | 4xp1C 4xp4C 4xp5C 4xp6C 4xp9C 4xpaC 4xpbC 4xpfC 4xpgC 4xphC 4m48S S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59977.500 Da / Num. of mol.: 1 / Mutation: V74A, D121G, S426M, 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-HEK293s / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6 |
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-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23306.586 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) |
-Sugars , 2 types, 6 molecules
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose #7: Sugar | ChemComp-NAG / | |
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-Non-polymers , 5 types, 6 molecules
#5: Chemical | ChemComp-Y01 / |
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#6: Chemical | ChemComp-42J / |
#8: Chemical | ChemComp-CLR / |
#9: Chemical | ChemComp-CL / |
#10: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.24 Å3/Da / Density % sol: 76.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 400 34%, Na MES 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. obs: 32436 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 114.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.801 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M48 Resolution: 3.36→38.6 Å
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Refinement step | Cycle: LAST / Resolution: 3.36→38.6 Å
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