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Yorodumi- PDB-4lde: Structure of beta2 adrenoceptor bound to BI167107 and an engineer... -
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-Basic information
Entry | Database: PDB / ID: 4lde | ||||||
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Title | Structure of beta2 adrenoceptor bound to BI167107 and an engineered nanobody | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/HYDROLASE / G protein coupled receptor / MEMBRANE PROTEIN-HYDROLASE complex | ||||||
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 / norepinephrine binding / positive regulation of autophagosome maturation / Adrenoceptors / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 / norepinephrine binding / positive regulation of autophagosome maturation / Adrenoceptors / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 / negative regulation of G protein-coupled receptor signaling pathway / 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 / bone resorption / positive regulation of bone mineralization / adenylate cyclase-activating adrenergic receptor signaling pathway / 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 / Cargo recognition for clathrin-mediated endocytosis / cell wall macromolecule catabolic process / Clathrin-mediated endocytosis / lysozyme / lysozyme activity / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / receptor complex / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / endosome / cell surface receptor signaling pathway / endosome membrane / early endosome / lysosome / Ub-specific processing proteases / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / membrane / 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: 2.79 Å | ||||||
Authors | Ring, A.M. / Manglik, A. / Kruse, A.C. / Enos, M.D. / Weis, W.I. / Garcia, K.C. / Kobilka, B.K. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Adrenaline-activated structure of beta 2-adrenoceptor stabilized by an engineered nanobody. Authors: Ring, A.M. / Manglik, A. / Kruse, A.C. / Enos, M.D. / Weis, W.I. / Garcia, K.C. / Kobilka, B.K. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lde.cif.gz | 247.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lde.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/4lde ftp://data.pdbj.org/pub/pdb/validation_reports/ld/4lde | HTTPS FTP |
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-Related structure data
Related structure data | 4ldlC 4ldoC 3p0gS 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
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 53471.039 Da / Num. of mol.: 1 Fragment: UNP residues 29-348 with a deletion of residues 235-263 Mutation: C918T, C962A, M1096T, M1098T, N1157E, C1265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: ADRB2, E, ADRB2R, B2AR / Plasmid: pVL1392 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00720, UniProt: P07550, lysozyme |
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#2: Antibody | Mass: 12949.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Engineered fragment / Source: (gene. exp.) Lama glama (llama) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
-Non-polymers , 4 types, 87 molecules
#3: Chemical | ChemComp-P0G / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-1WV / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.35 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.5 Details: 100 mM MES pH 6.2-6.7, 40-100 mM ammonium phosphate dibasic, 18-24% PEG400, 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: Dec 13, 2012 |
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: 2.79→38.4 Å / Num. obs: 25028 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1953 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P0G Resolution: 2.79→38.4 Å / SU ML: 0.43 / σ(F): 1.49 / Phase error: 28.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→38.4 Å
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Refine LS restraints |
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LS refinement shell |
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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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