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Yorodumi- PDB-5d5a: In meso in situ serial X-ray crystallography structure of the Bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d5a | |||||||||
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Title | In meso in situ serial X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K | |||||||||
Components | Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor | |||||||||
Keywords | Membrane Protein/Hydrolase / MEMBRANE PROTEIN / HYDROLASE / 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: 2.4826 Å | |||||||||
Authors | Huang, C.-Y. / Olieric, V. / Warshamanage, R. / Liu, X. / Kobilka, B. / Kay Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||
Funding support | Ireland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d5a.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d5a.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 5d5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5a ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5a | HTTPS FTP |
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-Related structure data
Related structure data | 5d52C 5d53C 5d54C 5d56C 5d57C 5d58C 5d59C 5d5bC 5d5cC 5d5dC 5d5eC 5d5fC 2rh1S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 56601.438 Da / Num. of mol.: 1 Mutation: N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A 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 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose |
-Non-polymers , 8 types, 68 molecules
#3: Chemical | ChemComp-CAU / ( | ||||||||||||
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#4: Chemical | #5: Chemical | ChemComp-ACM / | #6: Chemical | #7: Chemical | ChemComp-PLM / | #8: Chemical | ChemComp-12P / | #9: Chemical | ChemComp-SO4 / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.63 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 30-35 %(v/v) PEG 400, 0.1-0.2 M Na2SO4, 0.1 M bis-tris propane pH 6.5-7.0 and 5-7 %(v/v) 1,4-butanediol PH range: pH 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0322 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0322 Å / Relative weight: 1 |
Reflection | Resolution: 2.4826→50 Å / Num. obs: 23086 / % possible obs: 95.1 % / Redundancy: 5.7 % / Net I/σ(I): 7.27 |
Reflection shell | Resolution: 2.4826→2.57 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.11 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2rh1 Resolution: 2.4826→43.96 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.43 / 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: 2.4826→43.96 Å
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Refine LS restraints |
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LS refinement shell |
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