|Entry||Database: PDB / ID: 2omi|
|Title||Structure of human insulin cocrystallized with protamine|
|Keywords||HORMONE / insulin NPH microcrystals / hormone|
|Function / homology|
Function and homology information
Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / Regulation of insulin secretion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / IRS activation / Signal attenuation / Insulin receptor signalling cascade / COPI-mediated anterograde transport / Regulation of gene expression in beta cells / Insulin processing ...Synthesis, secretion, and deacylation of Ghrelin / Signaling by Insulin receptor / Regulation of insulin secretion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / IRS activation / Signal attenuation / Insulin receptor signalling cascade / COPI-mediated anterograde transport / Regulation of gene expression in beta cells / Insulin processing / Amyloid fiber formation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Insulin receptor recycling / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / negative regulation of NAD(P)H oxidase activity / positive regulation of respiratory burst / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of blood vessel diameter / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of lipid biosynthetic process / regulation of transmembrane transporter activity / positive regulation of dendritic spine maintenance / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of lipid catabolic process / negative regulation of protein secretion / negative regulation of protein oligomerization / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / regulation of cellular amino acid metabolic process / positive regulation of glycolytic process / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / endosome lumen / regulation of synaptic plasticity / positive regulation of insulin receptor signaling pathway / cognition / neuron projection maintenance / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of cytokine secretion / positive regulation of mitotic nuclear division / negative regulation of acute inflammatory response / regulation of protein localization / positive regulation of cell differentiation / positive regulation of long-term synaptic potentiation / activation of protein kinase B activity / positive regulation of glucose import / positive regulation of blood vessel diameter / hormone activity / negative regulation of protein catabolic process / acute-phase response / negative regulation of proteolysis / insulin receptor signaling pathway / positive regulation of protein localization to nucleus / insulin receptor binding / positive regulation of nitric-oxide synthase activity / glucose metabolic process / cell-cell signaling / Golgi lumen / wound healing / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / protease binding / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / cellular protein metabolic process / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Insulin / Insulin-like / Insulin family / Insulin, conserved site / Insulin/IGF/Relaxin family / Insulin-like superfamily / Insulin family signature.
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å|
|Authors||Norrman, M. / Schluckebier, G.|
|Citation||Journal: EUR.J.PHARM.SCI. / Year: 2007|
Title: Structural characterization of insulin NPH formulations.
Authors: Norrman, M. / Hubalek, F. / Schluckebier, G.
SummaryFull reportAbout validation report
|Date||Deposition: Jan 22, 2007 / Release: Mar 27, 2007|
|Structure viewer||Molecule: |
Downloads & links
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
E: Insulin A chain
F: Insulin B chain
G: Insulin A chain
H: Insulin B chain
I: Insulin A chain
J: Insulin B chain
K: Insulin A chain
L: Insulin B chain
-Protein/peptide , 2 types, 12 molecules A
C E G I K B D F H J L
Mass: 2383.698 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
Mass: 3433.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
-Non-polymers , 4 types, 120 molecules
Mass: 110.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O2 / Resorcinol
|#4: Chemical||#5: Chemical||#6: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 %|
|Crystal grow||Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 |
Details: 50mM resorcinol, 400mM NaCl, 1.0mg/ml protamine 30mM phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918 Å|
|Detector||Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 23, 2005|
|Radiation||Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.918 Å / Relative weight: 1|
|Reflection||Resolution: 2.24→30 Å / Num. all: 16106 / Num. obs: 15881 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.1|
|Reflection shell||Resolution: 2.24→2.4 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2781 / % possible all: 97.6|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: insulin hexamer R-conformation
Resolution: 2.24→29.1 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.045 / SU ML: 0.158 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK|
|Displacement parameters||Biso mean: 26.301 Å2|
|Refinement step||Cycle: LAST / Resolution: 2.24→29.1 Å|
|Refine LS restraints|
Refinement-ID: X-RAY DIFFRACTION
|LS refinement shell||Resolution: 2.24→2.296 Å / Total num. of bins used: 20 |
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