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Yorodumi- PDB-7ran: 5-HT2AR bound to a novel agonist in complex with a mini-Gq protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ran | ||||||
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Title | 5-HT2AR bound to a novel agonist in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / 5-HT2A receptor / serotonin receptor / G protein / GPCR / novel agonist / cryoEM | ||||||
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 / protein tyrosine kinase activator activity / behavioral response to cocaine / detection of temperature stimulus involved in sensory perception of pain / 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 / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / intracellular calcium ion homeostasis / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / memory / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of neuron apoptotic process / extracellular vesicle / G alpha (12/13) signalling events / positive regulation of peptidyl-tyrosine phosphorylation / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / virus receptor activity / retina development in camera-type eye / GTPase binding / presynaptic membrane / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation / chemical synaptic transmission / cytoplasmic vesicle / G alpha (s) signalling events / postsynaptic membrane / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / lysosomal membrane / axon / GTPase activity / dendrite Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
Authors | Barros-Alvarez, X. / Kim, K. / Panova, O. / Roth, B.L. / Skiniotis, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2022 Title: Bespoke library docking for 5-HT receptor agonists with antidepressant activity. Authors: Anat Levit Kaplan / Danielle N Confair / Kuglae Kim / Ximena Barros-Álvarez / Ramona M Rodriguiz / Ying Yang / Oh Sang Kweon / Tao Che / John D McCorvy / David N Kamber / James P Phelan / ...Authors: Anat Levit Kaplan / Danielle N Confair / Kuglae Kim / Ximena Barros-Álvarez / Ramona M Rodriguiz / Ying Yang / Oh Sang Kweon / Tao Che / John D McCorvy / David N Kamber / James P Phelan / Luan Carvalho Martins / Vladimir M Pogorelov / Jeffrey F DiBerto / Samuel T Slocum / Xi-Ping Huang / Jain Manish Kumar / Michael J Robertson / Ouliana Panova / Alpay B Seven / Autumn Q Wetsel / William C Wetsel / John J Irwin / Georgios Skiniotis / Brian K Shoichet / Bryan L Roth / Jonathan A Ellman / Abstract: There is considerable interest in screening ultralarge chemical libraries for ligand discovery, both empirically and computationally. Efforts have focused on readily synthesizable molecules, ...There is considerable interest in screening ultralarge chemical libraries for ligand discovery, both empirically and computationally. Efforts have focused on readily synthesizable molecules, inevitably leaving many chemotypes unexplored. Here we investigate structure-based docking of a bespoke virtual library of tetrahydropyridines-a scaffold that is poorly sampled by a general billion-molecule virtual library but is well suited to many aminergic G-protein-coupled receptors. Using three inputs, each with diverse available derivatives, a one pot C-H alkenylation, electrocyclization and reduction provides the tetrahydropyridine core with up to six sites of derivatization. Docking a virtual library of 75 million tetrahydropyridines against a model of the serotonin 5-HT receptor (5-HTR) led to the synthesis and testing of 17 initial molecules. Four of these molecules had low-micromolar activities against either the 5-HT or the 5-HT receptors. Structure-based optimization led to the 5-HTR agonists (R)-69 and (R)-70, with half-maximal effective concentration values of 41 nM and 110 nM, respectively, and unusual signalling kinetics that differ from psychedelic 5-HTR agonists. Cryo-electron microscopy structural analysis confirmed the predicted binding mode to 5-HTR. The favourable physical properties of these new agonists conferred high brain permeability, enabling mouse behavioural assays. Notably, neither had psychedelic activity, in contrast to classic 5-HTR agonists, whereas both had potent antidepressant activity in mouse models and had the same efficacy as antidepressants such as fluoxetine at as low as 1/40th of the dose. Prospects for using bespoke virtual libraries to sample pharmacologically relevant chemical space will be considered. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ran.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ran.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ran.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/7ran ftp://data.pdbj.org/pub/pdb/validation_reports/ra/7ran | HTTPS FTP |
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-Related structure data
Related structure data | 24378MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 38274.285 Da / Num. of mol.: 1 / Fragment: UNP residues 66-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTR2A, HTR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223 |
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#2: Protein | Mass: 28084.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
-Guanine nucleotide-binding protein ... , 2 types, 2 molecules CD
#3: Protein | Mass: 37416.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873 |
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#4: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768 |
-Antibody / Non-polymers , 2 types, 2 molecules E
#5: Antibody | Mass: 30552.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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#6: Chemical | ChemComp-3IQ / ( |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 5-HT2AR bound to a tetrahydropyridine agonist (R-69) in complex with heterotrimeric mini-Gq protein and single-chain variable fragment (scFv16) Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 17.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 57050 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60.01 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88393 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
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