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Yorodumi- PDB-3ny9: Crystal structure of the human beta2 adrenergic receptor in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ny9 | ||||||
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Title | Crystal structure of the human beta2 adrenergic receptor in complex with a novel inverse agonist | ||||||
Components | Beta-2 adrenergic receptor, Lysozyme | ||||||
Keywords | MEMBRANE PROTEIN / G Protein-coupled receptor / Lysozyme / Fusion / Transducer / Adrenergic / G-Proteins / Arrestins / Adrenalin / Compound 2 / Glycosylation / Palmitoylation / Phosphorylation / HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network / GPCR | ||||||
Function / homology | Function and homology information beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / positive regulation of autophagosome maturation / norepinephrine binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / positive regulation of autophagosome maturation / norepinephrine binding / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / neuronal dense core vesicle / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / bone resorption / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / regulation of sodium ion transport / viral release from host cell by cytolysis / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / positive regulation of cold-induced thermogenesis / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / lysozyme activity / Clathrin-mediated endocytosis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / lysosome / early endosome / receptor complex / cell surface receptor signaling pathway / 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 / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Fenalti, G. / Wacker, D. / Brown, M.A. / Katritch, V. / Abagyan, R. / Cherezov, V. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Conserved Binding Mode of Human beta(2) Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography Authors: Wacker, D. / Fenalti, G. / Brown, M.A. / Katritch, V. / Abagyan, R. / Cherezov, V. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ny9.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ny9.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ny9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ny9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3ny9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3ny9_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3ny9_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/3ny9 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3ny9 | HTTPS FTP |
-Related structure data
Related structure data | 3ny8C 3nyaC 3d4sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55957.926 Da / Num. of mol.: 1 Fragment: Chimeric protein of Beta-2 Adrenoreceptor 1-230, Lysozyme 2-161, Beta-2 adrenergic receptor 263-348 Mutation: E122W, N187E, C1054T, C1097A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: ADRB2, ADRB2R, B2AR, E / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P07550, UniProt: P00720 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-JSZ / | #4: Chemical | ChemComp-OLC / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 293 K Details: 100 mM Tris/HCl pH 7.5-8, 5% 1,4 butanediol, 220 mM Na-formate, 27% PEG 400, Lipidic Cubic Phase (LCP) Crystallization, temperature 293-295K PH range: 7.5-8.0 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.84→40 Å / Num. all: 13388 / Num. obs: 12234 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 3.84 % / Rsym value: 0.131 / Net I/σ(I): 7.08 | ||||||||||||||||||
Reflection shell | Resolution: 2.84→2.98 Å / Redundancy: 2.93 % / Mean I/σ(I) obs: 1.99 / Num. unique all: 1749 / Rsym value: 0.43 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3D4S Resolution: 2.84→37.77 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.156 / SU ML: 0.372 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.384 Å2
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Refinement step | Cycle: LAST / Resolution: 2.84→37.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.84→2.913 Å / Total num. of bins used: 20
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