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Yorodumi- PDB-1mpj: X-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mpj | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESENCE OF HELIX-STABILIZING AGENTS, THIOCYANATE, METHYLPARABEN AND PHENOL | ||||||
Components | (PHENOL INSULIN) x 2 | ||||||
Keywords | HORMONE | ||||||
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 / 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 DNA replication / 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 / Resolution: 2.3 Å | ||||||
Authors | Whittingham, J.L. / Dodson, E.J. / Moody, P.C.E. / Dodson, G.G. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: X-ray crystallographic studies on hexameric insulins in the presence of helix-stabilizing agents, thiocyanate, methylparaben, and phenol. Authors: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C. / Dodson, G.G. #1: Journal: Biopolymers / Year: 1992 Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol Authors: Smith, G.D. / Dodson, G.G. #2: Journal: Nature / Year: 1989 Title: Phenol Stabilizes More Helix in a New Symmetrical Zinc Insulin Hexamer Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mpj.cif.gz | 30.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mpj.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1mpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/1mpj ftp://data.pdbj.org/pub/pdb/validation_reports/mp/1mpj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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Atom site foot note | 1: PRO B 28 - LYS B 29 OMEGA = 267.87 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | |||||||||||||||
Components on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 |
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-Non-polymers , 4 types, 65 molecules
#3: Chemical | ChemComp-IPH / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.88 % |
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Crystal grow | *PLUS pH: 8 / Method: batch method |
Components of the solutions | *PLUS Conc.: 0.02 M / Common name: hydrochrolic acid |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 7.17 Å / Num. obs: 4058 / % possible obs: 96.9 % / Num. measured all: 8990 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.42 Å / % possible obs: 84.8 % / Mean I/σ(I) obs: 10.68 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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