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Yorodumi- PDB-6m47: X-ray structure of a Drosophila dopamine transporter with NET-lik... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m47 | |||||||||
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Title | X-ray structure of a Drosophila dopamine transporter with NET-like mutations (D121G/S426M/F471L) in tramadol bound form | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / neurotransmitter transporter / antibody fragment | |||||||||
Function / homology | Function and homology information Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / 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: 3.252 Å | |||||||||
Authors | Shabareesh, P. / Mallela, A.K. / Joseph, D. / Penmatsa, A. | |||||||||
Funding support | India, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of norepinephrine recognition and transport inhibition in neurotransmitter transporters. Authors: Pidathala, S. / Mallela, A.K. / Joseph, D. / Penmatsa, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m47.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m47.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m47_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6m47_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6m47_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6m47_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m47 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m47 | HTTPS FTP |
-Related structure data
Related structure data | 6m0fC 6m0zC 6m2rC 6m38C 6m3zC 4xnxS C: citing same article (ref.) S: Starting model for refinement |
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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: 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): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) |
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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): SF9 / Production host: Spodoptera frugiperda (fall armyworm) |
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 59844.352 Da / Num. of mol.: 1 / Mutation: D121G, S426M, F471L, V74A, L415A, DEL 162-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, fmn, CG8380 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6 |
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#4: Polysaccharide |
-Non-polymers , 7 types, 26 molecules
#5: Chemical | ChemComp-CLR / | ||||||||
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#6: Chemical | ChemComp-Y01 / | ||||||||
#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-F1U / ( | #10: Chemical | ChemComp-D10 / | #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.37 Å3/Da / Density % sol: 77.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M MOPS, pH 7.0, 30% PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.25→48.502 Å / Num. obs: 35898 / % possible obs: 97.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 98.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.071 / Rrim(I) all: 0.18 / Net I/σ(I): 10.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xnx Resolution: 3.252→48.502 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.56 Å2 / Biso mean: 89.3234 Å2 / Biso min: 55.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.252→48.502 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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