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Yorodumi- PDB-5lx9: CRYSTAL STRUCTURE OF HUMAN ADIPONECTIN RECEPTOR 2 IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lx9 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ADIPONECTIN RECEPTOR 2 IN COMPLEX WITH A C18 FREE FATTY ACID AT 2.4 ANGSTROM RESOLUTION | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / PROGESTIN AND ADIPOQ RECEPTOR FAMILY / INTEGRAL MEMBRANE PROTEIN / 7TM / CERAMIDASE | ||||||
Function / homology | Function and homology information adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Vasiliauskaite-Brooks, I. / Leyrat, C. / Hoh, F. / Granier, S. | ||||||
Funding support | France, 1items
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Citation | Journal: Nature / Year: 2017 Title: Structural insights into adiponectin receptors suggest ceramidase activity. Authors: Vasiliauskaite-Brooks, I. / Sounier, R. / Rochaix, P. / Bellot, G. / Fortier, M. / Hoh, F. / De Colibus, L. / Bechara, C. / Saied, E.M. / Arenz, C. / Leyrat, C. / Granier, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lx9.cif.gz | 239.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lx9.ent.gz | 198.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lx9 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lx9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Antibody , 2 types, 2 molecules AH
#1: Protein | Mass: 35020.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86V24*PLUS |
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#2: Antibody | Mass: 29841.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) |
-Non-polymers , 4 types, 541 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-OLA / | ||
#5: Chemical | ChemComp-OLB / ( #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.58 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 30-45% PEG 400, 0.1 M HEPES pH 7.0, and 50-100 mM potassium citrate, 0.01 mM AdipoRon |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→101.13 Å / Num. obs: 33584 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 41.55 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.527 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 10.2 % / Rmerge(I) obs: 5.681 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.489 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→101.13 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.294 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.187
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Displacement parameters | Biso mean: 50.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→101.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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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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