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Yorodumi- PDB-6mxt: Crystal structure of human beta2 adrenergic receptor bound to sal... -
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-Basic information
Entry | Database: PDB / ID: 6mxt | |||||||||
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Title | Crystal structure of human beta2 adrenergic receptor bound to salmeterol and Nb71 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN/HORMONE / G protein-coupled receptor / adrenergic receptor / asthma drug / active conformation / nanobody / SIGNALING PROTEIN-HORMONE complex / membrane protein | |||||||||
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 / neuronal dense core vesicle / diet induced thermogenesis / 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 / cell surface receptor signaling pathway / early endosome / 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 / MOLECULAR REPLACEMENT / Resolution: 2.95934213525 Å | |||||||||
Authors | Masureel, M. / Zou, Y. / Picard, L.P. / van der Westhuizen, E. / Mahoney, J.P. / Rodrigues, J.P.G.L.M. / Mildorf, T.J. / Dror, R.O. / Shaw, D.E. / Bouvier, M. ...Masureel, M. / Zou, Y. / Picard, L.P. / van der Westhuizen, E. / Mahoney, J.P. / Rodrigues, J.P.G.L.M. / Mildorf, T.J. / Dror, R.O. / Shaw, D.E. / Bouvier, M. / Pardon, E. / Steyaert, J. / Sunahara, R.K. / Weis, W.I. / Zhang, C. / Kobilka, B.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Structural insights into binding specificity, efficacy and bias of a beta2AR partial agonist. Authors: Masureel, M. / Zou, Y. / Picard, L.P. / van der Westhuizen, E. / Mahoney, J.P. / Rodrigues, J.P.G.L.M. / Mildorf, T.J. / Dror, R.O. / Shaw, D.E. / Bouvier, M. / Pardon, E. / Steyaert, J. / ...Authors: Masureel, M. / Zou, Y. / Picard, L.P. / van der Westhuizen, E. / Mahoney, J.P. / Rodrigues, J.P.G.L.M. / Mildorf, T.J. / Dror, R.O. / Shaw, D.E. / Bouvier, M. / Pardon, E. / Steyaert, J. / Sunahara, R.K. / Weis, W.I. / Zhang, C. / Kobilka, B.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mxt.cif.gz | 261.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mxt.ent.gz | 196.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/6mxt ftp://data.pdbj.org/pub/pdb/validation_reports/mx/6mxt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Antibody , 2 types, 2 molecules AN
#1: Protein | Mass: 53528.066 Da / Num. of mol.: 1 Fragment: chimera of T4 lysozyme fused to human beta2 adrenergic receptor (UNP residues 29-234,263-365) Mutation: M96T, M98T, N187E 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) References: UniProt: D9IEF7, UniProt: P07550, UniProt: P00720*PLUS, lysozyme |
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#2: Antibody | Mass: 13473.763 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) |
-Non-polymers , 8 types, 29 molecules
#3: Chemical | ChemComp-K5Y / | ||||||||||
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#4: Chemical | ChemComp-MG / | ||||||||||
#5: Chemical | #6: Chemical | ChemComp-OLC / ( | #7: Chemical | ChemComp-HTO / | #8: Chemical | ChemComp-OLA / | #9: Chemical | ChemComp-P33 / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.64 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / pH: 7.5 Details: 31-34% PEG400, 100 mM HEPES, pH 7.5, 1% 1,2,3-heptanetriol |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 18, 2012 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 18742 / % possible obs: 92.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.7347764892 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 1.52 |
Reflection shell | Resolution: 2.95→3.09 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1012 / Χ2: 7.5 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 4GBR & 4LDE Resolution: 2.95934213525→28.5196106168 Å / SU ML: 0.402084390742 / Cross valid method: FREE R-VALUE / σ(F): 1.38231122584 / Phase error: 24.3772282005
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.7137652891 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95934213525→28.5196106168 Å
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Refine LS restraints |
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LS refinement shell |
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