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Yorodumi- PDB-4xc4: Insulin co-crystallizes in the presence of it beta-cell chaperone... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xc4 | |||||||||
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Title | Insulin co-crystallizes in the presence of it beta-cell chaperone sulfatide | |||||||||
Components | (Insulin) x 2 | |||||||||
Keywords | HORMONE / Insulin-like fold / Insulin-like superfamily / diabetes | |||||||||
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: 1.499 Å | |||||||||
Authors | Bracey, A.W. / Magis, A.T. / Buschard, K. / Osterbye, T. / Bailey, K.M. / Ostrov, D.A. | |||||||||
Citation | Journal: To Be Published Title: Insulin co-crystallizes in the presence of it beta-cell chaperone sulfatide Authors: Bracey, A.W. / Magis, A.T. / Buschard, K. / Osterbye, T. / Bailey, K.M. / Ostrov, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xc4.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xc4.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xc4_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 4xc4_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 4xc4_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 4xc4_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xc4 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xc4 | HTTPS FTP |
-Related structure data
Related structure data | 3brr 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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-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 90-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: PAK721 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: PAK721 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 89 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.3M MAGNESIUM SULFATE, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9322 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 2007 |
Radiation | Monochromator: SI(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 |
Reflection | Resolution: 1.499→30 Å / Num. obs: 9224 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.499→1.5672 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 2.35 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BRR 3brr Resolution: 1.499→30 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.499→30 Å
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Refine LS restraints |
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LS refinement shell |
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