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Yorodumi- PDB-6kuw: Crystal structure of human alpha2C adrenergic G protein-coupled r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kuw | ||||||
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Title | Crystal structure of human alpha2C adrenergic G protein-coupled receptor. | ||||||
Components | Alpha-2C adrenergic receptor | ||||||
Keywords | SIGNALING PROTEIN / Alpha2c adrenergic receptor / antagonist / GPCR | ||||||
Function / homology | Function and homology information : / negative regulation of uterine smooth muscle contraction / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / receptor transactivation / epinephrine binding / negative regulation of norepinephrine secretion / alpha-2A adrenergic receptor binding / negative regulation of epinephrine secretion / regulation of sensory perception of pain ...: / negative regulation of uterine smooth muscle contraction / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / receptor transactivation / epinephrine binding / negative regulation of norepinephrine secretion / alpha-2A adrenergic receptor binding / negative regulation of epinephrine secretion / regulation of sensory perception of pain / Surfactant metabolism / Adrenoceptors / adrenergic receptor signaling pathway / plasma membrane => GO:0005886 / regulation of insulin secretion / axon terminus / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of vasoconstriction / positive regulation of neuron differentiation / activation of protein kinase B activity / female pregnancy / G protein-coupled receptor activity / Adrenaline,noradrenaline inhibits insulin secretion / platelet activation / G alpha (z) signalling events / cell-cell signaling / G alpha (i) signalling events / positive regulation of MAPK cascade / endosome / G protein-coupled receptor signaling pathway / protein heterodimerization activity / neuronal cell body / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Chen, X.Y. / Wu, L.J. / Wu, D. / Zhong, G.S. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human alpha2C adrenergic G protein-coupled receptor. Authors: Chen, X.Y. / Wu, D. / Wu, L.J. / Han, G.W. / Guo, Y. / Zhong, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kuw.cif.gz | 393.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kuw.ent.gz | 322.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kuw ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kuw | HTTPS FTP |
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-Related structure data
Related structure data | 4s0vS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55508.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18825*PLUS |
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-Non-polymers , 5 types, 15 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-OLC / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: sodium phosphate monobasic (0.1M), Hepes pH6.5-6.9 (0.1M), PEG400 24-35% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 26778 / % possible obs: 94.4 % / Redundancy: 3.74 % / Biso Wilson estimate: 79.97 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.127 / Net I/σ(I): 8.15 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1692 / CC1/2: 0.604 / % possible all: 82.1 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4s0v Resolution: 2.8→47.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389
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Displacement parameters | Biso mean: 65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→47.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.91 Å / Total num. of bins used: 13
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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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