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Yorodumi- PDB-7bu6: Structure of human beta1 adrenergic receptor bound to norepinephr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bu6 | ||||||
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Title | Structure of human beta1 adrenergic receptor bound to norepinephrine and nanobody 6B9 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / G protein coupled receptor | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) Camelidae mixed library (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Xu, X. / Kaindl, J. / Clark, M. / Hubner, H. / Hirata, K. / Sunahara, R. / Gmeiner, P. / Kobilka, B.K. / Liu, X. | ||||||
Citation | Journal: Cell Res. / Year: 2021 Title: Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR. Authors: Xu, X. / Kaindl, J. / Clark, M.J. / Hubner, H. / Hirata, K. / Sunahara, R.K. / Gmeiner, P. / Kobilka, B.K. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bu6.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bu6.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/7bu6 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/7bu6 | HTTPS FTP |
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-Related structure data
Related structure data | 7btsC 7bu7C 7bvqC 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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Unit cell |
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-Components
-Protein / Antibody / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 57625.109 Da / Num. of mol.: 1 / Mutation: C944T,C987A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126, ADRB1, ADRB1R, B1AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9IEF7, lysozyme |
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#2: Antibody | Mass: 14020.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae mixed library (mammal) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 8 types, 16 molecules
#4: Chemical | ChemComp-E5E / | ||||||||||||
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#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-EPE / | #8: Chemical | ChemComp-480 / ( | #9: Chemical | ChemComp-CLR / | #10: Chemical | ChemComp-PG4 / | #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Sequence details | THE GENEBANK ENTRY NP_000675 IS A REFERENCE SEQUENCE FOR THE RESIDUES FROM 171TH to 462TH OF CHAIN A. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM HEPES, pH 7.5, 100-250 mM Sodium Sulfate, 39-43% PEG300, 10mM norepinephrine |
-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: Dec 12, 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: 2.7→50 Å / Num. obs: 32544 / % possible obs: 100 % / Redundancy: 41.6 % / Biso Wilson estimate: 56.67 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.32 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 0.99 / Num. unique obs: 3316 / CC1/2: 0.518 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lde Resolution: 2.7→19.98 Å / SU ML: 0.4112 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.68 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.98 Å
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Refine LS restraints |
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LS refinement shell |
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