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Yorodumi- PDB-6w2b: Anomalous bromine signal reveals the position of Br-paroxetine co... -
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-Basic information
Entry | Database: PDB / ID: 6w2b | |||||||||
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Title | Anomalous bromine signal reveals the position of Br-paroxetine complexed with the serotonin transporter at the central site | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / antidepressant / complex / transporter / antibody | |||||||||
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: 4.7 Å | |||||||||
Authors | Coleman, J.A. / Navratna, V. / Yang, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: Chemical and structural investigation of the paroxetine-human serotonin transporter complex. Authors: Jonathan A Coleman / Vikas Navratna / Daniele Antermite / Dongxue Yang / James A Bull / Eric Gouaux / Abstract: Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand binding of small-molecules to conformationally ...Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand binding of small-molecules to conformationally dynamic transporters like SERT often require thermostabilizing mutations and antibodies to stabilize a specific conformation, leading to questions about relationships of these structures to the bonafide conformation and inhibitor binding poses of wild-type transporter. To address these concerns, we determined the structures of ∆N72/∆C13 and ts2-inactive SERT bound to paroxetine analogues using single-particle cryo-EM and x-ray crystallography, respectively. We synthesized enantiopure analogues of paroxetine containing either bromine or iodine instead of fluorine. We exploited the anomalous scattering of bromine and iodine to define the pose of these inhibitors and investigated inhibitor binding to Asn177 mutants of ts2-active SERT. These studies provide mutually consistent insights into how paroxetine and its analogues bind to the central substrate-binding site of SERT, stabilize the outward-open conformation, and inhibit serotonin transport. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w2b.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w2b.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 6w2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w2b_validation.pdf.gz | 644.2 KB | Display | wwPDB validaton report |
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Full document | 6w2b_full_validation.pdf.gz | 659 KB | Display | |
Data in XML | 6w2b_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6w2b_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/6w2b ftp://data.pdbj.org/pub/pdb/validation_reports/w2/6w2b | HTTPS FTP |
-Related structure data
Related structure data | 6vrhC 6vrkC 6vrlC 6w2cC 6awnS 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
#1: Protein | Mass: 61703.789 Da / Num. of mol.: 1 / Fragment: UNP residues 76-618 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A4, HTT, SERT / Cell line (production host): Hek293 GnTi- / Production host: Homo sapiens (human) / References: UniProt: P31645 |
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#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) / Production host: Spodoptera frugiperda (fall armyworm) |
#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) |
#4: Sugar | ChemComp-NAG / |
#5: Chemical | ChemComp-RFS / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 50 mM Tris, pH 8.5, 20 mM sodium sulfate, 20 mM lithium chloride, 36% PEG400, 0.5% 6-aminohexanoic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2019 |
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 4.69→30 Å / Num. obs: 14667 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 330.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.136 / Net I/σ(I): 5.51 |
Reflection shell | Resolution: 4.69→4.82 Å / Rmerge(I) obs: 0.3393 / Num. unique obs: 1130 / CC1/2: 0.165 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6AWN Resolution: 4.7→29.76 Å / SU ML: 0.9316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.3396 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 362.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.7→29.76 Å
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Refine LS restraints |
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LS refinement shell |
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