+Open data
-Basic information
Entry | Database: PDB / ID: 6wh4 | |||||||||
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Title | Crystal structure of HTR2A with inverse agonist | |||||||||
Components | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 fusion | |||||||||
Keywords | MEMBRANE PROTEIN / HTR2A | |||||||||
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: 3.4 Å | |||||||||
Authors | Kim, K.L. / Che, T. / Krumm, B.E. / Roth, B.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell(Cambridge,Mass.) / Year: 2020 Title: Structure of a Hallucinogen-Activated Gq-Coupled 5-HT 2A Serotonin Receptor Authors: Kim, K.L. / Che, T. / Panova, O. / DiBerto, J.F. / Lyu, J. / Krumm, B.E. / Wacker, D. / Robertson, M.J. / Seven, A.B. / Nichols, D.E. / Shoichet, B.K. / Skiniotis, G. / Roth, B.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wh4.cif.gz | 272.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wh4.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/6wh4 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/6wh4 | HTTPS FTP |
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-Related structure data
Related structure data | 6wgtC 5tvnS 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 50534.918 Da / Num. of mol.: 3 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 , 6 types, 15 molecules
#2: Chemical | #3: Chemical | ChemComp-OLA / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-NDS / | #7: Chemical | ChemComp-1PE / | |
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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: 3.79 Å3/Da / Density % sol: 67.55 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / pH: 7 Details: 100 mM Tris (pH7.0) 380 mM potassium phosphate-monobasic 33% PEG 400 100 mM Guanidine HCL 300 mM NDSB-195 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 3→34.78 Å / Num. obs: 41269 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 65.18 Å2 / CC1/2: 0.994 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 3→3.12 Å / Num. unique obs: 4468 / CC1/2: 0.306 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TVN Resolution: 3.4→33.5 Å / SU ML: 0.4708 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.5739 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: 48.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→33.5 Å
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Refine LS restraints |
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LS refinement shell |
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