+Open data
-Basic information
Entry | Database: PDB / ID: 2r4r | ||||||
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Title | Crystal structure of the human beta2 adrenoceptor | ||||||
Components |
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Keywords | SIGNALING PROTEIN / transmembrane helix / G-protein coupled receptor / Glycoprotein / Lipoprotein / Palmitate / Phosphorylation / Receptor / Transducer | ||||||
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 / activation of adenylate cyclase activity / receptor-mediated endocytosis / response to cold / 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 / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / positive regulation of cold-induced thermogenesis / G alpha (s) signalling events / positive regulation of MAPK cascade / transcription by RNA polymerase II / lysosome / cell surface receptor signaling pathway / receptor complex / early endosome / endosome membrane / Ub-specific processing proteases / endosome / 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 | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å | ||||||
Authors | Rasmussen, S.G.F. / Choi, H.J. / Rosenbaum, D.M. / Kobilka, T.S. / Thian, F.S. / Edwards, P.C. / Burghammer, M. / Ratnala, V.R. / Sanishvili, R. / Fischetti, R.F. ...Rasmussen, S.G.F. / Choi, H.J. / Rosenbaum, D.M. / Kobilka, T.S. / Thian, F.S. / Edwards, P.C. / Burghammer, M. / Ratnala, V.R. / Sanishvili, R. / Fischetti, R.F. / Schertler, G.F. / Weis, W.I. / Kobilka, B.K. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Authors: Rasmussen, S.G.F. / Choi, H.J. / Rosenbaum, D.M. / Kobilka, T.S. / Thian, F.S. / Edwards, P.C. / Burghammer, M. / Ratnala, V.R. / Sanishvili, R. / Fischetti, R.F. / Schertler, G.F. / Weis, W.I. / 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 | 2r4r.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r4r.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/2r4r ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r4r | HTTPS FTP |
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-Related structure data
Related structure data | 2r4sC 1gzmS 1igtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41280.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / References: UniProt: P07550 |
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#2: Antibody | Mass: 23902.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 23236.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→86.4 Å / Num. all: 19903 / Num. obs: 19671 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 67.2 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1642 / % possible all: 94.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1gzm and 1igt Resolution: 3.4→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1751083.75 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 77.504 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |