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Yorodumi- PDB-3w80: Crystal structure of dodecamer human insulin with double C-axis l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w80 | ||||||
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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 negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
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. | ||||||
Citation | 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. #6: Journal: J.APPL.CRYSTALLOGR. / Year: 1989 Title: The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography Authors: Higashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w80.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w80.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 3w80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w80_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 3w80_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 3w80_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3w80_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/3w80 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/3w80 | HTTPS FTP |
-Related structure data
Related structure data | 3w7yS 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 on special symmetry positions |
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-Components
#1: Protein/peptide | 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 #2: Protein/peptide | 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 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.2 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 |
-Processing
Software |
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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
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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
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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