|Entry||Database: PDB / ID: 3w80|
|Title||Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell|
|Components||(Insulin) x 2|
|Keywords||HORMONE / Human insulin / glucose metabolism / secretion|
|Function / homology|
Function and homology information
Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of acute inflammatory response / COPI-mediated anterograde transport / positive regulation of dendritic spine maintenance / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / Regulation of insulin secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / positive regulation of nitric oxide mediated signal transduction / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / transport vesicle / neuron projection maintenance / endosome lumen / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of brown fat cell differentiation / regulation of synaptic plasticity / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / cognition / regulation of protein localization / positive regulation of cytokine production / activation of protein kinase B activity / positive regulation of glucose import / acute-phase response / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor signaling pathway / insulin receptor binding / positive regulation of protein localization to nucleus / vasodilation / Golgi lumen / glucose metabolic process / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of protein kinase B signaling / positive regulation of NF-kappaB transcription factor activity / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / regulation of transcription, DNA-templated / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å|
|Authors||Murayoshi, M. / Sasaki, K. / Sakabe, N. / Sakabe, K.|
Journal: To be Published
Title: Crystal structure of dodecamer insulin with double C-axis length of the hexamer 2 Zn insulin celll
Authors: Murayoshi, M. / Sasaki, K. / Sakabe, N. / Sakabe, K.
#1: Journal: NUCL INSTRUM METHODS PHYS RES A / Year: 2001
Title: Automatic Weissenberg data collection system for time-resolved protein crystallography
Authors: Sakabe, N. / Sakabe, K. / Higashi, T. / Igarashi, N. / Suzuki, M. / Watanabe, N. / Sasaki, K.
#2: Journal: J.SYNCHROTRON RADIAT. / Year: 1999
Title: Rotated-inclined focusing monochromator with simultaneous tuning of asymmetry factor and radius of curvature over a wide wavelength range
Authors: Watanabe, N. / Suzuki, M. / Higashi, Y. / Sakabe, N.
#3: Journal: J.SYNCHROTRON RADIAT. / Year: 1997
Title: Large-Format Imaging Plate and Weissenberg Camera for Accurate Protein Crystallographic Data Collection Using Synchrotron Radiation
Authors: Sakabe, K. / Sasaki, K. / Watanabe, N. / Suzuki, M. / Wang, Z.G. / Miyahara, J. / Sakabe, N.
#4: Journal: PHILOS.TRANS.R.SOC.LOND.B BIOL.SCI. / Year: 1988
Title: The structure of 2Zn pig insulin crystals at 1.5A resolution
Authors: Baker, E. / Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G. / Hodgkin, D.M.C. / Hubbard, E. / Isaacs, N.W. / Reynolds, C.D. / Sakabe, K. / Sakabe, N. / Vijayan, N.M.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1972
Title: A statistical evaluation of absorption
Authors: Katayama, C. / Sakabe, N. / Sakabe, K.
|Structure viewer||Molecule: |
Downloads & links
|Components on special symmetry positions|
Mass: 2383.698 Da / Num. of mol.: 4 / Fragment: UNP residues 90-110 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
Mass: 3433.953 Da / Num. of mol.: 4 / Fragment: UNP residues 25-54 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308
|#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 1.93 Å3/Da / Density % sol: 36.2 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.67 |
Details: 10mg/ml protein, 0.1M Sodium Citrate, 22%(v/v) DMF, 0.08%(w/v) Zinc chloride, pH 8.67, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6C / Wavelength: 1 Å|
|Detector||Type: Fully automatic high speed Weissenberg data collection system called Galaxy|
Detector: IMAGE PLATE / Date: Nov 5, 2003
Details: The vertically focusing 1m long bent mirror of Pt-coated fused silica is 21m from the SR source point and 7m from the focus point
|Radiation||Monochromator: Rotated-inclined focusing Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1 Å / Relative weight: 1|
|Reflection||Resolution: 1→50 Å / Num. obs: 90240 / Redundancy: 4.46 % / Rmerge(I) obs: 0.05476|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 3w7y
Resolution: 1.4→10 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.964 / SU ML: 0.065 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK|
|Displacement parameters||Biso mean: 24.619 Å2|
|Refinement step||Cycle: LAST / Resolution: 1.4→10 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 1.4→1.436 Å / Total num. of bins used: 20 |
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