+Open data
-Basic information
Entry | Database: PDB / ID: 2zpp | ||||||
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Title | Neutron crystal structure of cubic insulin at pD9 | ||||||
Components |
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Keywords | HORMONE / CUBIC / PORCINE INSULIN / Carbohydrate metabolism / Cleavage on pair of basic residues / Glucose metabolism / Secreted | ||||||
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 / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / 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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ishikawa, T. / Tanaka, I. / Niimura, N. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: An abnormal pK(a) value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis Authors: Ishikawa, T. / Chatake, T. / Morimoto, Y. / Maeda, M. / Kurihara, K. / Tanaka, I. / Niimura, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zpp.cif.gz | 30.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zpp.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zpp ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zpp | HTTPS FTP |
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-Related structure data
Related structure data | 1b2gS S: Starting model for refinement |
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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) / Tissue: 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) / Tissue: Pancreas / References: UniProt: P01315 |
#3: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 9 Details: 0.2M sodium phosphate, 10mM 3NaEDTA, pH 9.0, MICRODIALYSIS, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: NUCLEAR REACTOR / Type: OTHER / Wavelength: 2.9 Å |
Detector | Type: BIX-3 / Detector: IMAGE PLATE / Date: Jun 22, 2002 |
Radiation | Monochromator: ELLASTICALLY BENT SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→80 Å / Num. all: 3789 / Num. obs: 3747 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.145 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.72 / Num. unique all: 368 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B2G Resolution: 2.5→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints | Type: c_bond_d / Dev ideal: 0.008 |