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- PDB-5d5b: In meso X-ray crystallography structure of the Beta2-adrenergic r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d5b | |||||||||
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Title | In meso X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K | |||||||||
![]() | Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor | |||||||||
![]() | Membrane Protein/Hydrolase / MEMBRANE PROTEIN / HYDROLASE / Membrane Protein-Hydrolase complex | |||||||||
Function / homology | ![]() : / beta2-adrenergic receptor activity / 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 / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...: / beta2-adrenergic receptor activity / 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 / 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 / adrenergic receptor signaling pathway / endosome to lysosome transport / 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 / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / viral release from host cell by cytolysis / bone resorption / activation of adenylate cyclase activity / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / 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 / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / 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 / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, C.-Y. / Olieric, V. / Liu, X. / Kobilka, B. / Wang, M. / Caffrey, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d52C ![]() 5d53C ![]() 5d54C ![]() 5d56C ![]() 5d57C ![]() 5d58C ![]() 5d59C ![]() 5d5aC ![]() 5d5cC ![]() 5d5dC ![]() 5d5eC ![]() 5d5fC ![]() 2rh1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() Gene: ADRB2, ADRB2R, B2AR / Production host: ![]() ![]() |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose |
-Non-polymers , 6 types, 13 molecules ![](data/chem/img/CAU.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/ACM.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/ACM.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/SO4.gif)
#3: Chemical | ChemComp-CAU / ( | ||||
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#4: Chemical | ChemComp-BU1 / | ||||
#5: Chemical | ChemComp-ACM / | ||||
#6: Chemical | #7: Chemical | ChemComp-PLM / | #8: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.42 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 6835 / % possible obs: 99.6 % / Redundancy: 6.5 % / Net I/σ(I): 3.76 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 4.58 % / Mean I/σ(I) obs: 0.96 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2rh1 Resolution: 3.8→49.618 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.87 / 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: 3.8→49.618 Å
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Refine LS restraints |
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LS refinement shell |
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