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Yorodumi- PDB-1guj: Insulin at pH 2: structural analysis of the conditions promoting ... -
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-Basic information
Entry | Database: PDB / ID: 1guj | ||||||
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Title | Insulin at pH 2: structural analysis of the conditions promoting insulin fibre formation. | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE / METABOLIC ROLE / LOW PH / SULPHATE IONS | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / 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 / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / 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: 1.62 Å | ||||||
Authors | Whittingham, J.L. / Scott, D.J. / Chance, K. / Wilson, A. / Finch, J. / Brange, J. / Dodson, G.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Insulin at Ph2: Structural Analysis of the Conditions Promoting Insulin Fibre Formation Authors: Whittingham, J.L. / Scott, D.J. / Chance, K. / Wilson, A. / Finch, J. / Brange, J. / Dodson, G.G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of an Insulin Dimer in an Orthorhombic Crystal: The Structure Analysis of a Human Insulin Mutant (B9 Ser to Glu) Authors: Yao, Z.-P. / Zeng, Z.-H. / Li, H.-M. / Zhang, Y. / Feng, Y.-M. / Wang, D.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1guj.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1guj.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 1guj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1guj ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1guj | HTTPS FTP |
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-Related structure data
Related structure data | 4insS 1vks 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99815, 0.00858, -0.06016), Vector: |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308 #3: Chemical | #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: 2.2 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 2.1 Details: HANGING DROP VAPOUR DIFFUSION METHOD PROTEIN SOL: 5 MG/ML HUMAN INSULIN IN SULPHURIC ACID PH 2.1 RESERVOIR SOL: SULPHURIC ACID PH 2.1,0.025 M SODIUM SULPHATE | |||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→20 Å / Num. obs: 13079 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 9 / % possible all: 100 |
Reflection | *PLUS % possible obs: 91 % / Redundancy: 5.3 % |
Reflection shell | *PLUS % possible obs: 76.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 9.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4INS Resolution: 1.62→34.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.041 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.091 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→34.3 Å
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