+Open data
-Basic information
Entry | Database: PDB / ID: 8w1v | ||||||
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Title | The beta2 adrenergic receptor bound to a bitopic ligand | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / signal transduction / bitopic ligand / / SIGNALING PROTEIN / GPCR | ||||||
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 / 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 | Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Gaiser, B. / Danielsen, M. / Xu, X. / Jorgensen, K. / Fronik, P. / Marcher-Rorsted, E. / Wrobe, T. / Hirata, K. / Liu, X. / Mathiesen, J. / Pedersen, D. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Bitopic Ligands Support the Presence of a Metastable Binding Site at the beta 2 Adrenergic Receptor. Authors: Gaiser, B.I. / Danielsen, M. / Xu, X. / Ropke Jorgensen, K. / Fronik, P. / Marcher-Rorsted, E. / Wrobel, T.M. / Liu, X. / Mosolff Mathiesen, J. / Sejer Pedersen, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w1v.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w1v.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8w1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w1v_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8w1v_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8w1v_validation.xml.gz | 42 KB | Display | |
Data in CIF | 8w1v_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/8w1v ftp://data.pdbj.org/pub/pdb/validation_reports/w1/8w1v | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62208.852 Da / Num. of mol.: 2 / Mutation: N187E,C1054T,C1097A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720, lysozyme #2: Antibody | Mass: 13531.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm) #3: Chemical | Mass: 581.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H51N5O4 #4: Chemical | ChemComp-AV0 / | Has ligand of interest | 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: 3.29 Å3/Da / Density % sol: 62.57 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM Tris buffer (pH 8.0), 100 to 175 mM lithium sulfate, 38% to 42% PEG400, and 10 mM EDTA |
-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, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→48.44 Å / Num. obs: 40547 / % possible obs: 99.9 % / Redundancy: 55.5 % / Biso Wilson estimate: 54.78 Å2 / CC1/2: 0.984 / Net I/σ(I): 8.25 |
Reflection shell | Resolution: 3→3.1 Å / Num. unique obs: 6655 / CC1/2: 0.564 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.44 Å / SU ML: 0.4897 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5555 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.44 Å
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Refine LS restraints |
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LS refinement shell |
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