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Yorodumi- PDB-5i75: X-ray structure of the ts3 human serotonin transporter complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i75 | ||||||
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Title | X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at the central site and Br-citalopram at the allosteric site | ||||||
Components |
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Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / serotonergic synapse / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / cocaine binding / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / serotonin:sodium:chloride symporter activity / sodium ion binding ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / serotonergic synapse / Serotonin clearance from the synaptic cleft / positive regulation of serotonin secretion / cocaine binding / negative regulation of synaptic transmission, dopaminergic / sperm ejaculation / serotonin:sodium:chloride symporter activity / sodium ion binding / cellular response to cGMP / enteric nervous system development / negative regulation of organ growth / serotonin uptake / neurotransmitter transmembrane transporter activity / serotonin binding / monoamine transmembrane transporter activity / monoamine transport / conditioned place preference / vasoconstriction / brain morphogenesis / antiporter activity / neurotransmitter transport / syntaxin-1 binding / amino acid transport / nitric-oxide synthase binding / membrane depolarization / behavioral response to cocaine / social behavior / negative regulation of neuron differentiation / sodium ion transmembrane transport / endomembrane system / monoatomic cation channel activity / positive regulation of cell cycle / cellular response to retinoic acid / response to nutrient / platelet aggregation / memory / response to toxic substance / circadian rhythm / actin filament binding / integrin binding / response to estradiol / presynaptic membrane / postsynaptic membrane / response to hypoxia / endosome membrane / neuron projection / response to xenobiotic stimulus / membrane raft / focal adhesion / synapse / positive regulation of gene expression / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å | ||||||
Authors | Coleman, J.A. / Green, E.M. / Gouaux, E. | ||||||
Citation | Journal: Nature / Year: 2016 Title: X-ray structures and mechanism of the human serotonin transporter. Authors: Coleman, J.A. / Green, E.M. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i75.cif.gz | 404.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i75.ent.gz | 337.5 KB | Display | PDB format |
PDBx/mmJSON format | 5i75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i75_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5i75_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5i75_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 5i75_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i75 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i75 | HTTPS FTP |
-Related structure data
Related structure data | 5i66C 5i6xC 5i6zC 5i71C 5i73C 5i74C 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 BC
#2: Antibody | Mass: 23688.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) |
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#3: Antibody | Mass: 23718.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) |
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 61689.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Production host: Homo sapiens (human) / References: UniProt: P31645 |
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#5: Sugar |
-Non-polymers , 5 types, 5 molecules
#4: Chemical | ChemComp-68P / ( |
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#6: Chemical | ChemComp-CLR / |
#7: Chemical | ChemComp-C14 / |
#8: Chemical | ChemComp-69D / ( |
#9: Chemical | ChemComp-NA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris pH 8.5, 25-125 mM KCl, 32.5-34% PEG 400, 0.5% 6-aminohexanoic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→82.29 Å / Num. obs: 38122 / % possible obs: 99.5 % / Redundancy: 11 % / Rmerge(I) obs: 0.08439 / Net I/σ(I): 17.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→82.29 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 30.74 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.49→82.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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