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Yorodumi- PDB-4qkx: Structure of beta2 adrenoceptor bound to a covalent agonist and a... -
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-Basic information
Entry | Database: PDB / ID: 4qkx | ||||||
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Title | Structure of beta2 adrenoceptor bound to a covalent agonist and an engineered nanobody | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/IMMUNE SYSTEM / 7-transmembrane helices / Signal transduction / G proteins / Membrane / MEMBRANE PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information : / 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 ...: / 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) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å | ||||||
Authors | Weichert, D. / Kruse, A.C. / Manglik, A. / Hiller, C. / Zhang, C. / Huebner, H. / Kobilka, B.K. / Gmeiner, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Covalent agonists for studying G protein-coupled receptor activation. Authors: Weichert, D. / Kruse, A.C. / Manglik, A. / Hiller, C. / Zhang, C. / Hubner, H. / Kobilka, B.K. / Gmeiner, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qkx.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qkx.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/4qkx ftp://data.pdbj.org/pub/pdb/validation_reports/qk/4qkx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53436.035 Da / Num. of mol.: 1 Mutation: C919T, C962A, H1093C, M1096T, M1098T, N1187E, C1265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126, ADRB2, ADRB2R, B2AR / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: D9IEF7, UniProt: P07550, UniProt: P00720*PLUS, 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.) Lama glama (llama) / Gene: r9 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) | ||
#3: Chemical | #4: Chemical | ChemComp-35V / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.45 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.8 Details: 24-27 % PEG400, 100 mM Tris pH 7.8 to pH 8.4, 5-10 mM Sodium formate, lipidic cubic phase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2013 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→33.3 Å / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.29 Å2 |
-Processing
Software |
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Refinement | Resolution: 3.3→33.26 Å / FOM work R set: 0.7753 / SU ML: 0.52 / σ(F): 1.34 / Phase error: 29.13 / Stereochemistry target values: ML
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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 max: 198.6 Å2 / Biso mean: 101.1 Å2 / Biso min: 57.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→33.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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