+Open data
-Basic information
Entry | Database: PDB / ID: 2efa | ||||||
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Title | Neutron crystal structure of cubic insulin at pD6.6 | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE/GROWTH FACTOR / HORMONE / CUBIC PORCINE INSULIN / 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 / 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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ishikawa, T. / Tanaka, I. / Niimura, N. | ||||||
Citation | Journal: Chem.Phys. / Year: 2008 Title: A neutron crystallographic analysis of a cubic porcine insulin at pD 6.6 Authors: Ishikawa, T. / Chatake, T. / Ohnishi, Y. / Tanaka, I. / Kurihara, K. / Kuroki, R. / Niimura, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efa.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efa.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 2efa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efa ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efa | HTTPS FTP |
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-Related structure data
Related structure data | 1b2aS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Fragment: Insulin A chain / 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 / Fragment: Insulin B chain / 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 | Density Matthews: 3.55 Å3/Da / Density % sol: 65.39 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 6.6 Details: 0.2M Sodium phosphate, 8mM 3NaEDTA, pH 6.6(PD), MICRODIALYSIS, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: NUCLEAR REACTOR / Type: OTHER / Wavelength: 2.6 Å |
Detector | Type: BIX-4 / Detector: IMAGE PLATE / Date: Jul 22, 2005 |
Radiation | Monochromator: ELLASTICALLY BENT SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→80 Å / Num. all: 2845 / Num. obs: 2749 / % possible obs: 92 % / Observed criterion σ(I): 3 / Redundancy: 3.34 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.159 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.65 / Num. unique all: 267 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B2A Resolution: 2.7→80 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→80 Å
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Refine LS restraints | Type: c_bond_d / Dev ideal: 0.01 |