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Yorodumi- PDB-6n48: Structure of beta2 adrenergic receptor bound to BI167107, Nanobod... -
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-Basic information
Entry | Database: PDB / ID: 6n48 | ||||||
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Title | Structure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator | ||||||
Components |
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Keywords | SIGNALING PROTEIN / G protein coupled receptor / membrane protein | ||||||
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 / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / 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 / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / 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 RB59 (virus) Homo sapiens (human) Camelidae (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Liu, X. / Masoudi, A. / Kahsai, A.W. / Huang, L.Y. / Pani, B. / Hirata, K. / Ahn, S. / Lefkowitz, R.J. / Kobilka, B.K. | ||||||
Citation | Journal: Science / Year: 2019 Title: Mechanism of beta2AR regulation by an intracellular positive allosteric modulator. Authors: Liu, X. / Masoudi, A. / Kahsai, A.W. / Huang, L.Y. / Pani, B. / Staus, D.P. / Shim, P.J. / Hirata, K. / Simhal, R.K. / Schwalb, A.M. / Rambarat, P.K. / Ahn, S. / Lefkowitz, R.J. / Kobilka, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n48.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n48.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 6n48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n48_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6n48_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6n48_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 6n48_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/6n48 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/6n48 | HTTPS FTP |
-Related structure data
Related structure data | 4ldeS 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
#1: Protein | Mass: 53471.039 Da / Num. of mol.: 1 Fragment: chimera of lysozyme and B2AR (UNP residues 29-234,263-348) Mutation: M1096T, M1098T, N1187E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB59 (virus), (gene. exp.) Homo sapiens (human) Gene: e, RB59_126, ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A097J809, 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 Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli BL21(DE3) (bacteria) |
#3: Chemical | ChemComp-P0G / |
#4: Chemical | ChemComp-1WV / ( |
#5: Chemical | ChemComp-KBY / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.94 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 100 mM Tris-HCl, pH 8.0, 150-200 mM lithium acetate, 43-45% PEG400 |
-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: Jul 15, 2018 |
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: 3.2→48 Å / Num. obs: 16912 / % possible obs: 98.4 % / Redundancy: 31.35 % / CC1/2: 0.986 / Net I/σ(I): 8.95 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 1380 / CC1/2: 0.584 / % possible all: 91.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4LDE Resolution: 3.2→19.921 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.97 / 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: 3.2→19.921 Å
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Refine LS restraints |
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LS refinement shell |
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