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Yorodumi- PDB-7dhi: Cryo-EM structure of the partial agonist salbutamol-bound beta2 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dhi | ||||||
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Title | Cryo-EM structure of the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex. | ||||||
Components |
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Keywords | SIGNALING PROTEIN / G protein coupled receptor / Complex / Cryo-EM | ||||||
Function / homology | Function and homology information 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 / : / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / Activation of G protein gated Potassium channels / G-protein activation ...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 / : / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / 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 / norepinephrine binding / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / activation of transmembrane receptor protein tyrosine kinase activity / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / negative regulation of smooth muscle contraction / positive regulation of lipophagy / G alpha (q) signalling events / response to psychosocial stress / G alpha (i) signalling events / negative regulation of multicellular organism growth / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / PKA activation in glucagon signalling / hair follicle placode formation / adenylate cyclase binding / smooth muscle contraction / mu-type opioid receptor binding / developmental growth / corticotropin-releasing hormone receptor 1 binding / potassium channel regulator activity / intracellular transport / D1 dopamine receptor binding / Hedgehog 'off' state / positive regulation of bone mineralization / brown fat cell differentiation / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / bone resorption / activation of adenylate cyclase activity / adenylate cyclase activator activity / response to cold / receptor-mediated endocytosis / trans-Golgi network membrane / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / clathrin-coated endocytic vesicle membrane / G-protein beta/gamma-subunit complex binding / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / cognition / photoreceptor disc membrane / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / platelet aggregation / 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 / cellular response to prostaglandin E stimulus / cellular response to amyloid-beta / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of smell / signaling receptor complex adaptor activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) Lama glama (llama) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||
Authors | Yang, F. / Ling, S.L. / Zhou, Y.X. / Zhang, Y.N. / Lv, P. / Liu, S.L. / Fang, W. / Sun, W.J. / Hu, L.Y.A. | ||||||
Citation | Journal: Natl Sci Rev / Year: 2020 Title: Different Conformational Responses of the beta2-Adrenergic Receptor-Gs Complex upon Binding of the Partial Agonist Salbutamol or the Full Agonist Isoprenaline Authors: Yang, F. / Ling, S.L. / Zhou, Y.X. / Zhang, Y.N. / Lv, P. / Liu, S.L. / Fang, W. / Sun, W.J. / Hu, L.Y.A. / Zhang, L. / Shi, P. / Tian, C. | ||||||
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 | 7dhi.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dhi.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 7dhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dhi_validation.pdf.gz | 756.4 KB | Display | wwPDB validaton report |
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Full document | 7dhi_full_validation.pdf.gz | 760.5 KB | Display | |
Data in XML | 7dhi_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 7dhi_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/7dhi ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dhi | HTTPS FTP |
-Related structure data
Related structure data | 30681MC 7dhrC M: map data used to model this data 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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-Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG
#1: Protein | Mass: 45812.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63092 |
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#2: Protein | Mass: 37416.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62871 |
#3: Protein | Mass: 8805.155 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63212 |
-Antibody / Protein , 2 types, 2 molecules NR
#4: Antibody | Mass: 17057.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#5: Protein | Mass: 42042.906 Da / Num. of mol.: 1 Mutation: G16R,E27Q,C77V,M96T,M98T,E122W,C125V,N187E,C265A,C285A,C327S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550 |
-Non-polymers , 2 types, 3 molecules
#6: Chemical | ChemComp-68H / |
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#7: Water | ChemComp-HOH / |
-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 the partial agonist salbutamol-bound beta2 adrenergic receptor-Gs protein complex. Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 151.4 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
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: SPOT SCAN |
Electron lens | Mode: DARK FIELD |
Image recording | Electron dose: 57.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 455803 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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