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Yorodumi- PDB-1b2g: PH AFFECTS GLU B13 SWITCHING AND SULFATE BINDING IN CUBIC INSULIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b2g | ||||||
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Title | PH AFFECTS GLU B13 SWITCHING AND SULFATE BINDING IN CUBIC INSULIN CRYSTALS (PH 9.00 COORDINATES) | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / HORMONE / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å | ||||||
Authors | Diao, J.S. / Caspar, D.L.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding. Authors: Diao, J. #1: Journal: Biophys.J. / Year: 1992 Title: Conformational Changes in Cubic Insulin Crystals in the Ph Range 7-11 Authors: Gursky, O. / Badger, J. / Li, Y. / Caspar, D.L. #2: Journal: Biophys.J. / Year: 1992 Title: Monovalent Cation Binding in Cubic Insulin Crystals Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L. #4: Journal: Acta Crystallogr.,Sect.B / Year: 1991 Title: Structure of the Pig Insulin Dimer in the Cubic Crystal Authors: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C.T. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Water Structure in Cubic Insulin Crystals Authors: Badger, J. / Caspar, D.L. #6: Journal: J.Mol.Biol. / Year: 1978 Title: Zinc-Free Cubic Pig Insulin: Crystallization and Structure Determination Authors: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b2g.cif.gz | 21.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b2g.ent.gz | 14.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2g ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2g | HTTPS FTP |
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-Related structure data
Related structure data | 1b17C 1b18C 1b19C 1b2aC 1b2bC 1b2cC 1b2dC 1b2eC 1b2fC 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315 |
#3: 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: 3.53 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.00 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: 1M SODIUM SULFATE SOLUTION AT PH 9.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9.2 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55 Å / Num. obs: 8672 / % possible obs: 94.8 % / Redundancy: 4 % / Biso Wilson estimate: 21.33 Å2 / Rsym value: 0.065 |
Reflection | *PLUS Highest resolution: 1.8 Å / % possible obs: 94.85 % / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.8→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 23.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å / Total num. of bins used: 15
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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