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Yorodumi- PDB-6awo: X-ray structure of the ts3 human serotonin transporter complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6awo | ||||||
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Title | X-ray structure of the ts3 human serotonin transporter complexed with sertraline at the central site | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Neurotransmitter transporter / antidepressant | ||||||
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 / immunoglobulin complex, circulating / membrane depolarization / behavioral response to cocaine / immunoglobulin receptor binding / 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 / complement activation, classical pathway / antigen binding / response to nutrient / platelet aggregation / memory / response to toxic substance / circadian rhythm / actin filament binding / integrin binding / response to estradiol / antibacterial humoral response / presynaptic membrane / postsynaptic membrane / blood microparticle / response to hypoxia / endosome membrane / neuron projection / immune response / response to xenobiotic stimulus / membrane raft / focal adhesion / synapse / positive regulation of gene expression / extracellular space / extracellular exosome / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.534 Å | ||||||
Authors | Coleman, J.A. / Gouaux, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2018 Title: Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Authors: Coleman, J.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 | 6awo.cif.gz | 210.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6awo.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 6awo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6awo_validation.pdf.gz | 857.5 KB | Display | wwPDB validaton report |
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Full document | 6awo_full_validation.pdf.gz | 883.2 KB | Display | |
Data in XML | 6awo_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 6awo_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/6awo ftp://data.pdbj.org/pub/pdb/validation_reports/aw/6awo | HTTPS FTP |
-Related structure data
Related structure data | 6awnC 6awpC 6awqC 5i6xS 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
-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 24853.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: HC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0F7R1P3 |
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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) / Gene: LC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0F7R5U8 |
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 61689.766 Da / Num. of mol.: 1 / Mutation: Y110A, I291A, T439S, C554A, C580A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P31645 |
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#5: Sugar |
-Non-polymers , 5 types, 6 molecules
#4: Chemical | ChemComp-SRE / ( | ||
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#6: Chemical | ChemComp-CLR / | ||
#7: Chemical | ChemComp-CL / | ||
#8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 50 mM Tris-HCl pH 8.5, 75 mM Li2SO4, 75 mM Na2SO4, 35% PEG 400, 0.5% 6-aminohexanoic acid |
-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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.53→40 Å / Num. obs: 33719 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.14 |
Reflection shell | Resolution: 3.53→3.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 1615 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5i6x Resolution: 3.534→39.855 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 36.48 / 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: 3.534→39.855 Å
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Refine LS restraints |
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LS refinement shell |
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