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Yorodumi- PDB-9bkj: Cholecystokinin 1 receptor (CCK1R) Y140A mutant, Gq chimera (mGsq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bkj | |||||||||||||||
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Title | Cholecystokinin 1 receptor (CCK1R) Y140A mutant, Gq chimera (mGsqi) complex | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / cholecystokinin / GPCR / cholesterol / mutant | |||||||||||||||
Function / homology | Function and homology information cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / neuropeptide hormone activity / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling / hair follicle placode formation ...cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / neuropeptide hormone activity / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling / hair follicle placode formation / mu-type opioid receptor binding / developmental growth / corticotropin-releasing hormone receptor 1 binding / intracellular transport / D1 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / Hedgehog 'off' state / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of mitotic spindle organization / cellular response to forskolin / forebrain development / cellular response to hormone stimulus / digestion / activation of adenylate cyclase activity / adenylate cyclase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / axonogenesis / trans-Golgi network membrane / Regulation of insulin secretion / G protein-coupled receptor binding / peptide binding / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / neuron migration / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / bone development / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / hormone activity / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / cognition / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to peptide hormone / photoreceptor disc membrane / platelet aggregation / 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 / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / GDP binding / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / sensory perception of smell / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / positive regulation of cold-induced thermogenesis / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||||||||
Authors | Cary, B.P. / Harikumar, K.G. / Zhao, P. / Desai, A.J. / Mobbs, J.M. / Toufaily, C. / Furness, S.G.B. / Christopoulos, A. / Belousoff, M.J. / Wootten, D. ...Cary, B.P. / Harikumar, K.G. / Zhao, P. / Desai, A.J. / Mobbs, J.M. / Toufaily, C. / Furness, S.G.B. / Christopoulos, A. / Belousoff, M.J. / Wootten, D. / Sexton, P.M. / Miller, L.J. | |||||||||||||||
Funding support | United States, Australia, 4items
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Citation | Journal: To Be Published Title: Cholesterol-dependent dynamic changes in the conformation of the type 1 cholecystokinin receptor affect ligand binding and G protein coupling Authors: Harikumar, K.G. / Zhao, P. / Cary, B.P. / Xu, X. / Desai, A.J. / Mobbs, J.I. / Toufaily, C. / Furness, S.G.B. / Christopoulos, A. / Belousoff, M.J. / Wootten, D. / Sexton, P.M. / Miller, L.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bkj.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bkj.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 9bkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bkj_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9bkj_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9bkj_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 9bkj_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/9bkj ftp://data.pdbj.org/pub/pdb/validation_reports/bk/9bkj | HTTPS FTP |
-Related structure data
Related structure data | 44642MC 9bkkC 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
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules BGA
#1: Protein | Mass: 37413.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873 |
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#2: Protein | Mass: 6375.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768 |
#5: Protein | Mass: 29144.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAS, GNAS1, GSP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63096, UniProt: P63092 |
-Protein/peptide / Protein / Non-polymers , 3 types, 3 molecules PR
#3: Protein/peptide | Mass: 1144.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06307 |
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#4: Protein | Mass: 47662.770 Da / Num. of mol.: 1 / Mutation: Y140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCKAR, CCKRA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32238 |
#6: Chemical | ChemComp-NH2 / |
-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: Complex of CCK1R (Y140A mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s. Type: COMPLEX Details: Single-chain fragment variable 16 (ScFv16) was included in the complex but left unmodeled. Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 0.150 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 20 mA, negative polarity / Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 defocus max: 1200 nm / Nominal defocus min: 600 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5884 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3580372 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279231 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7MBY Accession code: 7MBY / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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