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Yorodumi- PDB-7sqo: Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sqo | ||||||
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Title | Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and scFv16 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / CLASS A GPCR | ||||||
Function / homology | Function and homology information regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuropeptide receptor activity / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / feeding behavior ...regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuropeptide receptor activity / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / feeding behavior / locomotion / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / peptide hormone binding / neuropeptide signaling pathway / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to hormone stimulus / cellular response to forskolin / regulation of cytosolic calcium ion concentration / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptide binding / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GPER1 signaling / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / chemical synaptic transmission / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / synapse / nucleolus / GTP binding / magnesium ion binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å | ||||||
Authors | McGrath, A.P. / Kang, Y. / Flinspach, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular mechanism of the wake-promoting agent TAK-925. Authors: Jie Yin / Yanyong Kang / Aaron P McGrath / Karen Chapman / Megan Sjodt / Eiji Kimura / Atsutoshi Okabe / Tatsuki Koike / Yuhei Miyanohana / Yuji Shimizu / Rameshu Rallabandi / Peng Lian / ...Authors: Jie Yin / Yanyong Kang / Aaron P McGrath / Karen Chapman / Megan Sjodt / Eiji Kimura / Atsutoshi Okabe / Tatsuki Koike / Yuhei Miyanohana / Yuji Shimizu / Rameshu Rallabandi / Peng Lian / Xiaochen Bai / Mack Flinspach / Jef K De Brabander / Daniel M Rosenbaum / Abstract: The OX orexin receptor (OXR) is a highly expressed G protein-coupled receptor (GPCR) in the brain that regulates wakefulness and circadian rhythms in humans. Antagonism of OXR is a proven therapeutic ...The OX orexin receptor (OXR) is a highly expressed G protein-coupled receptor (GPCR) in the brain that regulates wakefulness and circadian rhythms in humans. Antagonism of OXR is a proven therapeutic strategy for insomnia drugs, and agonism of OXR is a potentially powerful approach for narcolepsy type 1, which is characterized by the death of orexinergic neurons. Until recently, agonism of OXR had been considered 'undruggable.' We harness cryo-electron microscopy of OXR-G protein complexes to determine how the first clinically tested OXR agonist TAK-925 can activate OXR in a highly selective manner. Two structures of TAK-925-bound OXR with either a G mimetic or G reveal that TAK-925 binds at the same site occupied by antagonists, yet interacts with the transmembrane helices to trigger activating microswitches. Our structural and mutagenesis data show that TAK-925's selectivity is mediated by subtle differences between OX and OX receptor subtypes at the orthosteric pocket. Finally, differences in the polarity of interactions at the G protein binding interfaces help to rationalize OXR's coupling selectivity for G signaling. The mechanisms of TAK-925's binding, activation, and selectivity presented herein will aid in understanding the efficacy of small molecule OXR agonists for narcolepsy and other circadian disorders. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sqo.cif.gz | 373.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sqo.ent.gz | 300 KB | Display | PDB format |
PDBx/mmJSON format | 7sqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sqo_validation.pdf.gz | 971.2 KB | Display | wwPDB validaton report |
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Full document | 7sqo_full_validation.pdf.gz | 985.2 KB | Display | |
Data in XML | 7sqo_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 7sqo_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/7sqo ftp://data.pdbj.org/pub/pdb/validation_reports/sq/7sqo | HTTPS FTP |
-Related structure data
Related structure data | 25389MC 7sr8C 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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-Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG
#2: Protein | Mass: 40459.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63096 |
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#3: Protein | Mass: 39151.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62871 |
#4: Protein | Mass: 7563.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63212 |
-Protein / Antibody , 2 types, 2 molecules RE
#1: Protein | Mass: 50733.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCRTR2 / Production host: Spodoptera (butterflies/moths) / References: UniProt: O43614 |
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#5: Antibody | Mass: 26277.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Trichoplusia ni (cabbage looper) |
-Non-polymers , 2 types, 5 molecules
#6: Chemical | ChemComp-OLA / #7: Chemical | ChemComp-A6F / | |
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-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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Vitrification | 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 FIELD / Nominal magnification: 130000 X / Cs: 2.7 mm |
Image recording | Electron dose: 43.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) Details: Cryo-EM movie stacks were collected on a Titan Krios microscope operated at 300 kV under EFTEM mode. Nanoprobe with 1um illumination area was used. Data were recorded on a postGIF Gatan K2 ...Details: Cryo-EM movie stacks were collected on a Titan Krios microscope operated at 300 kV under EFTEM mode. Nanoprobe with 1um illumination area was used. Data were recorded on a postGIF Gatan K2 summit camera at a nominal magnification of 130,000, using super-resolution counting model. Bioquantum energy filter was operated in the zero-energy-loss mode with an energy slit width of 20 eV. |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
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EM software |
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Image processing | Details: Frames 2-30 were used during dose-weighted movie frame alignment to reduce effects of beam-induced motion. Parameters of the FEI Titan Krios contrast transfer function were subsequently ...Details: Frames 2-30 were used during dose-weighted movie frame alignment to reduce effects of beam-induced motion. Parameters of the FEI Titan Krios contrast transfer function were subsequently estimated for each micrograph. A total 647,261 particles were auto-picked using Template Picker and extracted in 220 x 220 pixels box using cryoSPARC. All particles were subject to three rounds of reference-free 2D classification. Four initial model were made using cryoSPARC based on selected particles. The final 3D refinement in cryoSPARC2 used 251,169 particles, producing a reconstruction with 3.17A nominal resolution. | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 647261 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.17 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 251169 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 107.86 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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