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Yorodumi- PDB-7wc4: Crystal structure of serotonin 2A receptor in complex with serotonin -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wc4 | ||||||||||||
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Title | Crystal structure of serotonin 2A receptor in complex with serotonin | ||||||||||||
Components | 5-hydroxytryptamine receptor 2A,5-hydroxytryptamine receptor 2A,5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 | ||||||||||||
Keywords | MEMBRANE PROTEIN / serotonin 2A receptor / serotonin / 5-HT | ||||||||||||
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 / artery smooth muscle contraction / serotonin receptor signaling pathway / Serotonin receptors ...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 / artery smooth muscle contraction / serotonin receptor signaling pathway / Serotonin receptors / 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 / protein tyrosine kinase activator activity / behavioral response to cocaine / detection of temperature stimulus involved in sensory perception of pain / negative regulation of potassium ion transport / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / : / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / dendritic shaft / caveola / glycolytic process / memory / intracellular calcium ion homeostasis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / virus receptor activity / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / G alpha (q) signalling events / chemical synaptic transmission / postsynaptic membrane / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / axon / neuronal cell body / glutamatergic synapse / dendrite / positive regulation of cell population proliferation / protein-containing complex binding / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Cao, D. / Yu, J. / Wang, H. / Luo, Z. / Liu, X. / He, L. / Qi, J. / Fan, L. / Tang, L. / Chen, Z. ...Cao, D. / Yu, J. / Wang, H. / Luo, Z. / Liu, X. / He, L. / Qi, J. / Fan, L. / Tang, L. / Chen, Z. / Li, J. / Cheng, J. / Wang, S. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Science / Year: 2022 Title: Structure-based discovery of nonhallucinogenic psychedelic analogs. Authors: Cao, D. / Yu, J. / Wang, H. / Luo, Z. / Liu, X. / He, L. / Qi, J. / Fan, L. / Tang, L. / Chen, Z. / Li, J. / Cheng, J. / Wang, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wc4.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wc4.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/7wc4 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/7wc4 | HTTPS FTP |
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-Related structure data
Related structure data | 7wc5C 7wc6C 7wc7C 7wc8C 7wc9C 6a93S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42056.258 Da / Num. of mol.: 1 / Mutation: S162K,M164W,M1007W,R1098I,H1102I,R1106G,S372N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTR2A, HTR2, HTR2A, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223 |
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-Non-polymers , 6 types, 10 molecules
#2: Chemical | #3: Chemical | ChemComp-1PE / | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-SRO / | #7: Water | ChemComp-HOH / | |
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-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: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase Details: 100 mM Tris-HCl , 100 mM sodium acetate trihydrate, 30% (v/v) polyethylene glycol 400 (PEG400), 4% (v/v) Polypropylene glycol P 400 PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→48.05 Å / Num. obs: 8511 / % possible obs: 99 % / Redundancy: 9.1 % / CC1/2: 0.996 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1456 / CC1/2: 0.323 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A93 Resolution: 3.2→48.05 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.898 / SU B: 31.711 / SU ML: 0.502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 274.5 Å2 / Biso mean: 71.165 Å2 / Biso min: 30.31 Å2
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Refinement step | Cycle: final / Resolution: 3.2→48.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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