+Open data
-Basic information
Entry | Database: PDB / ID: 7vod | ||||||||||||
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Title | Crystal structure of 5-HT2AR in complex with cariprazine | ||||||||||||
Components | 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 | ||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / Dopamine Receptor / serotonin receptor / cariprazine / antipsychotic | ||||||||||||
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 / electron transport chain / 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 / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / iron ion binding / axon / neuronal cell body / glutamatergic synapse / dendrite / 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) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||||||||
Authors | Chen, Z. / Fan, L. / Wang, H. / Yu, J. / Lu, D. / Qi, J. / Nie, F. / Luo, Z. / Liu, Z. / Cheng, J. / Wang, S. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat.Neurosci. / Year: 2022 Title: Structure-based design of a novel third-generation antipsychotic drug lead with potential antidepressant properties. Authors: Chen, Z. / Fan, L. / Wang, H. / Yu, J. / Lu, D. / Qi, J. / Nie, F. / Luo, Z. / Liu, Z. / 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 | 7vod.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vod.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/7vod ftp://data.pdbj.org/pub/pdb/validation_reports/vo/7vod | HTTPS FTP |
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-Related structure data
Related structure data | 7voeC 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
#1: Protein | Mass: 41958.074 Da / Num. of mol.: 1 / Mutation: S162K,N164W,M1007W,R1098I,H1102I,R1106G,S372N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTR2A, HTR2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223, UniProt: P0ABE7 | ||||||
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#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-7RU / | 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: 2.97 Å3/Da / Density % sol: 58.62 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / Details: 100 mM Tris/HCl, 100 mM Potassium formate, 30% PEG / PH range: 6.5-7.0 |
-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: Jul 6, 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: 3.3→48.42 Å / Num. obs: 7889 / % possible obs: 97.8 % / Redundancy: 14.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.273 / Rpim(I) all: 0.072 / Rrim(I) all: 0.283 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1449 / CC1/2: 0.396 / Rpim(I) all: 0.472 / Rrim(I) all: 1.35 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A93 Resolution: 3.3→48.42 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.924 / SU B: 28.929 / SU ML: 0.437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.5 / 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: 220.53 Å2 / Biso mean: 77.625 Å2 / Biso min: 11.73 Å2
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Refinement step | Cycle: final / Resolution: 3.3→48.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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