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Yorodumi- PDB-7ezm: Cryo-EM structure of an activated Cholecystokinin A receptor (CCK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ezm | ||||||
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Title | Cryo-EM structure of an activated Cholecystokinin A receptor (CCKAR)-Gq complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Cholecystokinin A receptor / Gq complex / CCK-8 | ||||||
Function / homology | Function and homology information cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / entrainment of circadian clock / phospholipase C-activating dopamine receptor signaling pathway / regulation of platelet activation / phototransduction, visible light ...cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / entrainment of circadian clock / phospholipase C-activating dopamine receptor signaling pathway / regulation of platelet activation / phototransduction, visible light / regulation of canonical Wnt signaling pathway / glutamate receptor signaling pathway / action potential / peptide hormone binding / photoreceptor outer segment / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / cellular response to hormone stimulus / forebrain development / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity / axonogenesis / G-protein beta/gamma-subunit complex binding / Peptide ligand-binding receptors / Regulation of insulin secretion / G protein-coupled receptor binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / peptide binding / negative regulation of protein kinase activity / neuron migration / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G beta:gamma signalling through CDC42 / response to peptide hormone / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GDP binding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / blood coagulation / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / midbody / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / nuclear membrane / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / protein stabilization / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / synapse Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Liu, Q.F. / Yang, D.H. / Zhuang, Y.W. / Croll, T.I. / Cai, X.Q. / Duan, J. / Dai, A.T. / Yin, W.C. / Ye, C.Y. / Zhou, F.L. ...Liu, Q.F. / Yang, D.H. / Zhuang, Y.W. / Croll, T.I. / Cai, X.Q. / Duan, J. / Dai, A.T. / Yin, W.C. / Ye, C.Y. / Zhou, F.L. / Wu, B.L. / Zhao, Q. / Xu, H.E. / Wang, M.W. / Jiang, Y. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Ligand recognition and G-protein coupling selectivity of cholecystokinin A receptor Authors: Liu, Q. / Yang, D. / Zhuang, Y. / Croll, T.I. / Cai, X. / Dai, A. / He, X. / Duan, J. / Yin, W. / Ye, C. / Zhou, F. / Wu, B. / Zhao, Q. / Xu, H.E. / Wang, M.W. / Jiang, Y. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ezm.cif.gz | 214.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ezm.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ezm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ezm_validation.pdf.gz | 705 KB | Display | wwPDB validaton report |
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Full document | 7ezm_full_validation.pdf.gz | 712.3 KB | Display | |
Data in XML | 7ezm_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 7ezm_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/7ezm ftp://data.pdbj.org/pub/pdb/validation_reports/ez/7ezm | HTTPS FTP |
-Related structure data
Related structure data | 31389MC 7ezhC 7ezkC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 41268.910 Da / Num. of mol.: 1 / Mutation: G208A,A331S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAQ, GAQ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63096, UniProt: P50148 |
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#3: Protein | Mass: 47886.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCKAR, CCKRA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32238 |
-Guanine nucleotide-binding protein ... , 2 types, 2 molecules BG
#2: Protein | Mass: 38744.371 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 / Protein/peptide , 2 types, 2 molecules HP
#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: Spodoptera frugiperda (fall armyworm) |
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#6: Protein/peptide | Mass: 1291.428 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) |
-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: Cryo-EM structure of an activated Cholecystokinin A receptor (CCKAR)-Gq complex Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | 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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 555628 / Symmetry type: POINT |