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Yorodumi- PDB-2rh1: High resolution crystal structure of human B2-adrenergic G protei... -
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-Basic information
Entry | Database: PDB / ID: 2rh1 | |||||||||
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Title | High resolution crystal structure of human B2-adrenergic G protein-coupled receptor. | |||||||||
Components | beta-2-adrenergic receptor/T4-lysozyme chimera | |||||||||
Keywords | MEMBRANE PROTEIN / HYDROLASE / GPCR / 7TM / adrenergic / fusion / lipidic cubic phase / lipidic / mesophase / cholesterol / membrane protein / MEMBRANE PROTEIN - HYDROLASE COMPLEX / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network | |||||||||
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 | Homo sapiens (human) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | |||||||||
Authors | Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. ...Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR) | |||||||||
Citation | Journal: Science / Year: 2007 Title: High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Authors: Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. / Stevens, R.C. #1: Journal: To be Published Title: GPCR Engineering Yields High-Resolution Structural Insights into beta2 Adrenergic Receptor Function. Authors: Rosenbaum, D.M. / Cherezov, V. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Yao, X.J. / Weis, W.I. / Stevens, R.C. / Kobilka, B.K. | |||||||||
History |
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Remark 600 | HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR ...HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR RESPECTIVE CYSTEINE RESIDUES. | |||||||||
Remark 999 | SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED ...SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED TO ORIGINAL SEQUENCE DATABASE RESIDUE NUMBERS (2-161) OF THE LYSOZYME PART IN COORDINATES TO DISTINGUISH THE LYSOZYME PART IN THE CHAIN. THEREFORE THE RESIDUES OF LYSOZYME PART HAVE NUMBERS A1002-A1161. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rh1.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rh1.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 2rh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rh1_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2rh1_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2rh1_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2rh1_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/2rh1 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/2rh1 | HTTPS FTP |
-Related structure data
Related structure data | 1u19S 2lzmS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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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Details | Authors state that the biological unit is unknown |
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 56601.438 Da / Num. of mol.: 1 / Mutation: N187E, C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Genus: Homo, T4-like viruses / Species: , Enterobacteria phage T4 sensu lato / Strain: , Description: The construct has been obtained by overlapping extension PCR Gene: ADRB2, ADRB2R, B2AR / E / Plasmid: pFastbac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 8 types, 63 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CAU / ( | #5: Chemical | #6: Chemical | ChemComp-ACM / | #7: Chemical | #8: Chemical | ChemComp-PLM / | #9: Chemical | ChemComp-12P / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 27 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.98 % Description: This structure is a part of the Roadmap/PSI community outreach program, not a specific PSI target. |
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Crystal grow | Temperature: 293 K / Method: lipidic mesophase / pH: 6.75 Details: 30-35% v/v PEG 400, 0.1-0.2 M Na2SO4, 0.1 M Bis-tris propane pH 6.5-7.0, 5-7% 1,4-Butanediol, 8-10% Cholesterol, 52-50% Monoolein, pH 6.75, LIPIDIC MESOPHASE, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→20 Å / Num. all: 26705 / Num. obs: 26506 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.908 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.62 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1U19, 2LZM Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.501 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Water #548 has strong difference density but weak 2Fo-Fc density.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.912 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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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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