+Open data
-Basic information
Entry | Database: PDB / ID: 6a93 | ||||||
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Title | Crystal structure of 5-HT2AR in complex with risperidone | ||||||
Components | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information protein localization to cytoskeleton / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / serotonin receptor signaling pathway / Serotonin receptors / artery smooth muscle contraction ...protein localization to cytoskeleton / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / serotonin receptor signaling pathway / Serotonin receptors / artery smooth muscle contraction / cell body fiber / urinary bladder smooth muscle contraction / serotonin binding / negative regulation of synaptic transmission, glutamatergic / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / temperature homeostasis / regulation of dopamine secretion / detection of temperature stimulus involved in sensory perception of pain / protein tyrosine kinase activator activity / behavioral response to cocaine / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of potassium ion transport / activation of phospholipase C activity / positive regulation of fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / release of sequestered calcium ion into cytosol / positive regulation of vasoconstriction / presynaptic modulation of chemical synaptic transmission / positive regulation of glycolytic process / dendritic shaft / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / glycolytic process / memory / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / cytoplasmic vesicle / postsynaptic membrane / G alpha (q) signalling events / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / iron ion binding / axon / neuronal cell body / dendrite / glutamatergic synapse / heme binding / positive regulation of cell population proliferation / protein-containing complex binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kimura, T.K. / Asada, H. / Inoue, A. / Kadji, F.M.N. / Im, D. / Mori, C. / Arakawa, T. / Hirata, K. / Nomura, Y. / Nomura, N. ...Kimura, T.K. / Asada, H. / Inoue, A. / Kadji, F.M.N. / Im, D. / Mori, C. / Arakawa, T. / Hirata, K. / Nomura, Y. / Nomura, N. / Aoki, J. / Iwata, S. / Shimamura, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2019 Title: Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine. Authors: Kimura, K.T. / Asada, H. / Inoue, A. / Kadji, F.M.N. / Im, D. / Mori, C. / Arakawa, T. / Hirata, K. / Nomura, Y. / Nomura, N. / Aoki, J. / Iwata, S. / Shimamura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a93.cif.gz | 306 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a93.ent.gz | 246.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/6a93 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a93 | HTTPS FTP |
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-Related structure data
Related structure data | 6a94C 2rh1S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41931.051 Da / Num. of mol.: 2 / Mutation: S162K, M164W, R120I, H124I, R128G, M29W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: HTR2A, HTR2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223, UniProt: P0ABE7 |
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-Non-polymers , 5 types, 9 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: Chemical | ChemComp-PLM / | |
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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: 3.21 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.707→46.241 Å / Num. obs: 29971 / % possible obs: 83.96 % / Redundancy: 22.4 % / CC1/2: 0.993 / Net I/σ(I): 6.63 |
Reflection shell | Resolution: 2.707→2.8 Å / CC1/2: 0.677 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RH1 Resolution: 3→46.241 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 26.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→46.241 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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