+Open data
-Basic information
Entry | Database: PDB / ID: 3pds | ||||||
---|---|---|---|---|---|---|---|
Title | Irreversible Agonist-Beta2 Adrenoceptor Complex | ||||||
Components | Fusion protein Beta-2 adrenergic receptor/Lysozyme | ||||||
Keywords | Membrane Protein/Hydrolase / GPCR / signaling / beta adrenergic agonist / fusion protein / Membrane Protein-Hydrolase complex | ||||||
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 / endosome to lysosome transport / adrenergic receptor signaling pathway / 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 / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / bone resorption / viral release from host cell by cytolysis / activation of adenylate cyclase activity / receptor-mediated endocytosis / response to cold / 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 / amyloid-beta binding / positive regulation of cold-induced thermogenesis / G alpha (s) signalling events / host cell cytoplasm / positive regulation of MAPK cascade / transcription by RNA polymerase II / 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 / nucleus / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.-J. / DeVree, B.T. / Sunahara, R.K. ...Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.-J. / DeVree, B.T. / Sunahara, R.K. / Chae, P.S. / Gellman, S.H. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Caffrey, M. / Gmeiner, P. / Kobilka, B.K. | ||||||
Citation | Journal: Nature / Year: 2011 Title: Structure and function of an irreversible agonist-beta(2) adrenoceptor complex Authors: Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.J. / Devree, B.T. / Sunahara, R.K. / Chae, P.S. / Gellman, S.H. / Dror, R.O. / ...Authors: Rosenbaum, D.M. / Zhang, C. / Lyons, J.A. / Holl, R. / Aragao, D. / Arlow, D.H. / Rasmussen, S.G.F. / Choi, H.J. / Devree, B.T. / Sunahara, R.K. / Chae, P.S. / Gellman, S.H. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Caffrey, M. / Gmeiner, P. / Kobilka, B.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pds.cif.gz | 194 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pds.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/3pds ftp://data.pdbj.org/pub/pdb/validation_reports/pd/3pds | HTTPS FTP |
---|
-Related structure data
Related structure data | 2rh1S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52453.273 Da / Num. of mol.: 1 / Mutation: H93C,N187E,C265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720, lysozyme |
---|---|
#2: Chemical | ChemComp-ERC / |
#3: Chemical | ChemComp-CLR / |
#4: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 19 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.7 Details: 26 %(v/v) PEG 400, 200 mM Li2SO4, 4 %(v/v) DMSO, 3.5 %(v/v) 1,4-butandediol, 100 mM MES pH 6.7, Lipidic Cubic Phase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2010 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→65 Å / Num. all: 10025 / Num. obs: 9385 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.202 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2 / % possible all: 94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RH1 Resolution: 3.5→65.21 Å / Cor.coef. Fo:Fc: 0.8466 / Cor.coef. Fo:Fc free: 0.7701 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.879 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→65.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.91 Å / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|