+Open data
-Basic information
Entry | Database: PDB / ID: 1zeg | ||||||
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Title | STRUCTURE OF B28 ASP INSULIN IN COMPLEX WITH PHENOL | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE / METABOLIC ROLE / CHEMICAL ACTIVITY / INSULIN MUTANT / CROSS-LINK / GLUCOSE METABOLISM / DIABETES | ||||||
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 / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / nitric oxide-cGMP-mediated signaling / 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 / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / nitric oxide-cGMP-mediated signaling / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic 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 / positive regulation of brown fat cell differentiation / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / 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 long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of nitric-oxide synthase activity / 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 / hormone activity / negative regulation of protein catabolic process / cognition / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / 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 / Resolution: 1.6 Å | ||||||
Authors | Whittingham, J.L. / Edwards, E.J. / Antson, A.A. / Clarkson, J.M. / Dodson, G.G. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Interactions of phenol and m-cresol in the insulin hexamer, and their effect on the association properties of B28 pro --> Asp insulin analogues. Authors: Whittingham, J.L. / Edwards, D.J. / Antson, A.A. / Clarkson, J.M. / Dodson, G.G. #1: Journal: Structure / Year: 1995 Title: Role of C-Terminal B-Chain Residues in Insulin Assembly: The Structure of Hexameric Lysb28Prob29-Human Insulin Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D. #2: Journal: Biopolymers / Year: 1992 Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol Authors: Smith, G.D. / 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 | 1zeg.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zeg.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/1zeg ftp://data.pdbj.org/pub/pdb/validation_reports/ze/1zeg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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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 / Mutation: CHAIN B, D, P28D 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: 3451.926 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, P28D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 115 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 1.95 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: batch method / pH: 6.5 Details: BATCH METHOD, COMPOSITION OF CRYSTALLISATION SOLUTION 3.5 MG INSULIN + 0.5 ML 0.02M HCL + 0.05 ML 0.12M ZINC ACETATE + 0.25 ML 0.2M TRI-SODIUM CITRATE + 0.2 ML 2.5% (W/V) PHENOL IN ETHANOL + ...Details: BATCH METHOD, COMPOSITION OF CRYSTALLISATION SOLUTION 3.5 MG INSULIN + 0.5 ML 0.02M HCL + 0.05 ML 0.12M ZINC ACETATE + 0.25 ML 0.2M TRI-SODIUM CITRATE + 0.2 ML 2.5% (W/V) PHENOL IN ETHANOL + 60 MG NACL, pH 6.5, batch method | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 50 ℃ / Method: batch method / PH range low: 6.8 / PH range high: 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→14.7 Å / Num. obs: 11469 / % possible obs: 98.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.023 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.038 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 74966 |
Reflection shell | *PLUS % possible obs: 97.4 % |
-Processing
Software |
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Refinement | Starting model: B28ASP INSULIN WITH M-CRESOL DIMER Resolution: 1.6→14.7 Å / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 20.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→14.7 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 11469 / Rfactor all: 0.145 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |