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Yorodumi- PDB-1uz9: Crystallographic and solution studies of N-lithocholyl insulin: a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uz9 | ||||||
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Title | Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins. | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | INSULIN / DIABETES MELLITUS / INSULIN FAMILY / HORMONE DISEASE MUTATION | ||||||
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 / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 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: 1.6 Å | ||||||
Authors | Whittingham, J.L. / Jonassen, I. / Havelund, S. / Roberts, S.M. / Dodson, E.J. / Verma, C.S. / Wilkinson, A.J. / Dodson, G.G. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystallographic and Solution Studies of N-Lithocholyl Insulin: A New Generation of Prolonged-Acting Human Insulins Authors: Whittingham, J.L. / Jonassen, I. / Havelund, S. / Roberts, S.M. / Dodson, E.J. / Verma, C.S. / Wilkinson, A.J. / Dodson, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uz9.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uz9.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1uz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/1uz9 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/1uz9 | HTTPS FTP |
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-Related structure data
Related structure data | 1xdaS 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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Unit cell |
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Components on special symmetry positions |
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Details | THE DODECAMER IS OF THE A-B HEXAMER TYPE WITH 6 A AND 6B CHAINS LINKED BY DISULFIDE BONDS THAT CAN BE GENERATEDBY APPLICATION OF SYMMETRY OPERATORS 2, 3, 10, 11 AND 12FROM REMARK 290 ABOVE. |
-Components
-Protein/peptide , 2 types, 2 molecules AB
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Fragment: INSULIN A CHAIN, RESIDUES 90-110 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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#2: Protein/peptide | Mass: 3332.849 Da / Num. of mol.: 1 / Fragment: INSULIN B CHAIN, RESIDUES 25-53 / Source method: obtained synthetically Details: PEPTIDE LINK BETWEEN B 29 SIDE CHAIN AND LITHOCHOLYL GROUP Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
-Non-polymers , 5 types, 54 molecules
#3: Chemical | ChemComp-CRS / |
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#4: Chemical | ChemComp-UZ9 / ( |
#5: Chemical | ChemComp-ZN / |
#6: Chemical | ChemComp-CL / |
#7: Water | ChemComp-HOH / |
-Details
Compound details | INSULIN DECREASES BLOOD GLUCOSE CONCENTRATION AND INCREASES CELL PERMEABILITY TO MONOSACCHARIDES, ...INSULIN DECREASES BLOOD GLUCOSE CONCENTRAT |
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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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 8 Details: 0.5 M TRIS-HCL PH 8.0 0.1M TRI-SODIUM CITRATE, 2MM ZINC ACETATE, 0.05% W/V M-CRESOL |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→24 Å / Num. obs: 7689 / % possible obs: 98 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 5 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 14 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XDA Resolution: 1.6→24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.48 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.09 / 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: 19.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→24 Å
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