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Yorodumi- PDB-7xk9: Structure of human beta2 adrenergic receptor bound to constrained... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xk9 | ||||||
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Title | Structure of human beta2 adrenergic receptor bound to constrained isoproterenol | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / GPCR | ||||||
Function / homology | Function and homology information desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity ...desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / bone resorption / viral release from host cell by cytolysis / activation of adenylate cyclase activity / response to cold / receptor-mediated endocytosis / peptidoglycan catabolic process / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / cellular response to amyloid-beta / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / lysosome / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M. / Stobel, A. / Maul, L. / Mayer, D. / Hubner, H. / Venkatakrishnan, A. / Dror, R. ...Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M. / Stobel, A. / Maul, L. / Mayer, D. / Hubner, H. / Venkatakrishnan, A. / Dror, R. / Kobilka, B.K. / Sunahara, R. / Liu, X. / Gmeiner, P. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Constrained catecholamines gain beta 2 AR selectivity through allosteric effects on pocket dynamics. Authors: Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M.J. / Stossel, A. / Maul, L. / Mayer, D. / Hubner, H. / Hirata, K. / Venkatakrishnan, A.J. / Dror, R.O. / Kobilka, B.K. / Sunahara, R.K. / Liu, X. / Gmeiner, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xk9.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xk9.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/7xk9 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/7xk9 | HTTPS FTP |
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-Related structure data
Related structure data | 7xkaC 4ldeS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53471.039 Da / Num. of mol.: 1 / Mutation: C918T,C962A,M1096T,M1098T,N1157E,C1265A Source method: isolated from a genetically manipulated source Details: Chimera protein Source: (gene. exp.) Enterobacteria phage T4, (gene. exp.) Homo sapiens (human) Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00720, UniProt: P07550, lysozyme |
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#2: Antibody | Mass: 12949.375 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) |
#3: Chemical | ChemComp-GJ6 / ( |
#4: Chemical | ChemComp-NA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.21 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100mM Tris-HCl, pH 8.0, 150-200mM lithium acetate, 43-45% PEG 400 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2018 |
Radiation | Monochromator: liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→19.96 Å / Num. obs: 14451 / % possible obs: 98.85 % / Redundancy: 32 % / Biso Wilson estimate: 63.8 Å2 / CC1/2: 0.972 / Net I/σ(I): 6.66 |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 5.8 % / Num. unique obs: 1410 / CC1/2: 0.566 / % possible all: 97.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4LDE Resolution: 3.4→19.96 Å / SU ML: 0.4714 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5105 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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