+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+67 | ||||||
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Title | Structure of beta2 adrenergic receptor fused to a Gs peptide | ||||||
Components | Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera | ||||||
Keywords | MEMBRANE PROTEIN / G protein coupled Receptor | ||||||
Function / homology | Function and homology information 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 / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity ...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 / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / 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 / positive regulation of protein kinase A signaling / neuronal dense core vesicle / PKA activation in glucagon signalling / adenylate cyclase binding / hair follicle placode formation / developmental growth / smooth muscle contraction / D1 dopamine receptor binding / intracellular transport / renal water homeostasis / Hedgehog 'off' state / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / regulation of sodium ion transport / viral release from host cell by cytolysis / cellular response to glucagon stimulus / adenylate cyclase activator activity / regulation of insulin secretion / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / clathrin-coated endocytic vesicle membrane / bone development / positive regulation of protein serine/threonine kinase activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein activity / platelet aggregation / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / cognition / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / cellular response to amyloid-beta / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / cellular response to prostaglandin E stimulus / cell wall macromolecule catabolic process / sensory perception of smell / heterotrimeric G-protein complex / lysozyme / Cargo recognition for clathrin-mediated endocytosis / lysozyme activity / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (i) signalling events / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / early endosome / lysosome / receptor complex / cell surface receptor signaling pathway / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / G protein-coupled receptor signaling pathway / apical plasma membrane / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage RB59 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Liu, X. / Xu, X. / Hilger, D. / Tiemann, J. / Liu, H. / Du, Y. / Hirata, K. / Sun, X. / Guixa-Gonzalez, R. / Mathiesen, J. ...Liu, X. / Xu, X. / Hilger, D. / Tiemann, J. / Liu, H. / Du, Y. / Hirata, K. / Sun, X. / Guixa-Gonzalez, R. / Mathiesen, J. / Hildebrand, P. / Kobilka, B. | ||||||
Citation | Journal: Cell / Year: 2019 Title: Structural Insights into the Process of GPCR-G Protein Complex Formation. Authors: Liu, X. / Xu, X. / Hilger, D. / Aschauer, P. / Tiemann, J.K.S. / Du, Y. / Liu, H. / Hirata, K. / Sun, X. / Guixa-Gonzalez, R. / Mathiesen, J.M. / Hildebrand, P.W. / 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 | 6e67.cif.gz | 372 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e67.ent.gz | 304.4 KB | Display | PDB format |
PDBx/mmJSON format | 6e67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e67_validation.pdf.gz | 947.7 KB | Display | wwPDB validaton report |
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Full document | 6e67_full_validation.pdf.gz | 955 KB | Display | |
Data in XML | 6e67_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 6e67_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e67 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e67 | HTTPS FTP |
-Related structure data
Related structure data | 6eg8C 4ldeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60158.539 Da / Num. of mol.: 2 Fragment: beta-2 (UNP residues 1-232), lysozyme (UNP residues 2-161), GS (UNP residues 1024-1036) Mutation: M96T, M98T, N187E, C22A, C1054T, C1097A,M96T, M98T, N187E, C1054T, C1097A,M96T, M98T, N187E, C1054T, C1097A,M96T, M98T, N187E, C1054T, C1097A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (virus) Gene: ADRB2, ADRB2R, B2AR, e, RB59_126, GNAS, GNAS1, GSP / Plasmid: pvl1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P07550, UniProt: A0A097J809, UniProt: P63092, lysozyme #2: Chemical | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.9 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 100 mM Bis-Tris, pH 7.0, 75-125 mM ammonium acetate, 50-75 mM potassium fluoride, 38-42% PEG400, 6% ethylene glycol, 1.5% 1,2-propaneiol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 11, 2016 |
Radiation | Monochromator: liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→45.6 Å / Num. obs: 16163 / % possible obs: 99 % / Redundancy: 7.5 % / CC1/2: 0.98 / Net I/σ(I): 4.15 |
Reflection shell | Resolution: 3.7→3.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 1257 / CC1/2: 0.51 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4LDE Resolution: 3.7→19.98 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.31 / 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: 3.7→19.98 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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