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Yorodumi- PDB-5lxg: Revised crystal structure of the human adiponectin receptor 1 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lxg | |||||||||
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Title | Revised crystal structure of the human adiponectin receptor 1 in an open conformation | |||||||||
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 / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of epithelial to mesenchymal transition / negative regulation of non-canonical NF-kappaB signal transduction / fatty acid oxidation ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / leptin-mediated signaling pathway / negative regulation of epithelial cell migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of epithelial to mesenchymal transition / negative regulation of non-canonical NF-kappaB signal transduction / fatty acid oxidation / regulation of lipid metabolic process / regulation of glucose metabolic process / positive regulation of insulin receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell growth / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / protein kinase binding / identical protein binding / membrane / 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: 2.73 Å | |||||||||
Authors | Leyrat, C. / Vasiliauskaite-Brooks, I. / 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 | 5lxg.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lxg.ent.gz | 178 KB | Display | PDB format |
PDBx/mmJSON format | 5lxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lxg_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 5lxg_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 5lxg_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5lxg_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lxg ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lxg | HTTPS FTP |
-Related structure data
Related structure data | 5lwyC 5lx9C 5lxaC 3wxv 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 , 1 types, 1 molecules A
#1: Protein | Mass: 35040.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADIPOR1, PAQR1, TESBP1A, CGI-45 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96A54 |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 13160.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: E.COLI CELL-FREE PROTEIN SYNTHESIS / Production host: Escherichia coli (E. coli) |
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#3: Antibody | Mass: 11647.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: E.COLI CELL-FREE PROTEIN SYNTHESIS / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 172 molecules
#4: Chemical | ChemComp-ZN / | ||
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#5: Chemical | #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: 2.78 Å3/Da / Density % sol: 55.78 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 100mM Bicine, 100mM MgCl2, 30% PEG400, pH 8.0, Lipidic mesophase method, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 23, 2013 |
Radiation | Monochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→97.06 Å / Num. obs: 17815 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 52.37 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.934 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WXV 3wxv Resolution: 2.73→26.66 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.115 / SU Rfree Blow DPI: 0.312 / SU Rfree Cruickshank DPI: 0.312
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Displacement parameters | Biso mean: 74.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.73→26.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.73→2.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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