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Yorodumi- PDB-7wgd: X-ray structure of thermostabilized Drosophila dopamine transport... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wgd | ||||||
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Title | X-ray structure of thermostabilized Drosophila dopamine transporter with GABA transporter1-like substitutions in the binding site, in substrate-free form. | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / neurotransmitter transporter / antibody fragment / GABA transporter | ||||||
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: 3.2 Å | ||||||
Authors | Joseph, D. / Penmatsa, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Embo J. / Year: 2022 Title: Structural insights into GABA transport inhibition using an engineered neurotransmitter transporter. Authors: Joseph, D. / Nayak, S.R. / Penmatsa, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgd.cif.gz | 207.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgd.ent.gz | 158.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgd ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgd | HTTPS FTP |
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-Related structure data
Related structure data | 7wgtC 7wlwC 4xnuS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60144.594 Da / Num. of mol.: 1 Mutation: (thermostabilizing)V74A, V275A, V311A, L415A, G538L; (GAT1 like) F43Y, D46G, V120L, D121N, S422Q, G425T, S426V, A117S, F325L, V327S, E384S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, fmn, CG8380 / Plasmid: pEG Bacmam / Cell line (production host): 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) / Plasmid: pFastbac dual / 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) / Plasmid: pFastbac dual / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) |
-Non-polymers , 5 types, 24 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-Y01 / | #7: Chemical | ChemComp-CLR / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 5.33 Å3/Da / Density % sol: 78 % / Description: long rods |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1M MOPS pH 7.2, 36% PEG 600 / PH range: 7.0-7.5 / Temp details: cold room crystallization (4-6C) |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo stream at 100K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→48.43 Å / Num. obs: 38565 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 95.67 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.717 / Rpim(I) all: 0.219 / Rrim(I) all: 0.753 / Net I/σ(I): 9.1 / Num. measured all: 497543 / Scaling rejects: 14930 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XNU Resolution: 3.2→48.43 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.76 / 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: 177.35 Å2 / Biso mean: 85.9383 Å2 / Biso min: 51.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→48.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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