+Open data
-Basic information
Entry | Database: PDB / ID: 9ins | ||||||
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Title | MONOVALENT CATION BINDING IN CUBIC INSULIN CRYSTALS | ||||||
Components |
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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: 1.7 Å | ||||||
Authors | Badger, J. / Dodson, G.G. | ||||||
Citation | Journal: Biophys.J. / Year: 1992 Title: Monovalent cation binding to cubic insulin crystals Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.D. #1: 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. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Water Structure in Cubic Insulin Crystals Authors: Badger, J. / Caspar, D.L.D. #3: 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 | 9ins.cif.gz | 19.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ins.ent.gz | 15.8 KB | Display | PDB format |
PDBx/mmJSON format | 9ins.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/9ins ftp://data.pdbj.org/pub/pdb/validation_reports/in/9ins | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: WATER 24 IS PROBABLY A PARTIALLY OCCUPIED SODIUM ION. ANOTHER SODIUM SITE WITH VERY LOW OCCUPANCY OVERLAPS THE MAJOR CONFORMATION OF HIS B10 (SEE REF 3). 2: SEE REMARK 5. | |||||||||
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 genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.21 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→10 Å / Rfactor obs: 0.178 / σ(F): 2 Details: BY COMPARISON WITH MULTIPLE DATA SETS FROM BOVINE CUBIC INSULIN COLLECTED IN THE PH RANGE 7 TO 11 (REFERENCE 1 AND UNPUBLISHED RESULTS) IT HAS BEEN POSSIBLE TO RELIABLY IDENTIFY ADDITIONAL ...Details: BY COMPARISON WITH MULTIPLE DATA SETS FROM BOVINE CUBIC INSULIN COLLECTED IN THE PH RANGE 7 TO 11 (REFERENCE 1 AND UNPUBLISHED RESULTS) IT HAS BEEN POSSIBLE TO RELIABLY IDENTIFY ADDITIONAL CONFORMATIONS FOR SEVERAL SIDE CHAINS THAT WERE NOT INCLUDED IN THE PUBLISHED (ACTA CRYSTALLOGR.) REPORT. THESE HAVE BEEN MODELED, THE ORDERED SOLVENT RATIONALIZED AND THE STRUCTURE REFINED FURTHER. THE R-FACTOR AND STEREOCHEMICAL PARAMETERS IN THIS ENTRY ARE FOR THIS NEW MODEL. IN THE ACTA CRYSTALLOGRAPHICA 1991 PUBLICATION (REFERENCE 2 ABOVE) REFERENCE IS MADE TO PROTEIN DATA BANK ENTRY 5INS. THE COORDINATES IN THIS ENTRY SUPERSEDE 5INS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |