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Yorodumi- PDB-6m2r: X-ray structure of a functional Drosophila dopamine transporter i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2r | |||||||||
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Title | X-ray structure of a functional Drosophila dopamine transporter in L-norepinephrine 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: 2.802 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 | 6m2r.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2r.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 6m2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m2r_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6m2r_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6m2r_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 6m2r_validation.cif.gz | 52.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2r ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2r | HTTPS FTP |
-Related structure data
Related structure data | 6m0fC 6m0zC 6m38C 6m3zC 6m47C 4xp1S 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, 2 molecules A
#1: Protein | Mass: 60114.523 Da / Num. of mol.: 1 Mutation: N-terminal deletion 24, V74A, Deletion 162-202, L415A, F471L 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: Sugar | ChemComp-DMU / |
-Non-polymers , 7 types, 110 molecules
#5: Chemical | ChemComp-Y01 / | ||||
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#6: Chemical | ChemComp-CLR / | ||||
#7: Chemical | ChemComp-LNR / | ||||
#8: Chemical | ChemComp-CL / | ||||
#9: Chemical | ChemComp-NA / #10: Chemical | #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: 5.36 Å3/Da / Density % sol: 77.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 32% PEG 600, 0.1M MOPS pH6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→48.41 Å / Num. obs: 57216 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 71.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Net I/σ(I): 15.1 / Num. measured all: 352537 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XP1 Resolution: 2.802→48.4 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.85 Å2 / Biso mean: 64.2973 Å2 / Biso min: 36.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.802→48.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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