+Open data
-Basic information
Entry | Database: PDB / ID: 1znj | ||||||
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Title | INSULIN, MONOCLINIC CRYSTAL FORM | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE / METABOLIC ROLE / CHEMICAL ACTIVITY / INSULIN 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Turkenburg, M.G.W. / Whittingham, J.L. / Turkenburg, J.P. / Dodson, G.G. / Derewenda, U. / Smith, G.D. / Dodson, E.J. / Derewenda, Z.S. / Xiao, B. | ||||||
Citation | Journal: To be Published Title: Structure Determination and Refinement of Two Crystal Forms of Native Insulins Authors: Turkenburg, J.P. / Whittingham, J.L. / Derewenda, U. / Derewenda, Z.S. / Dodson, E.J. / Dodson, G.G. / Smith, G.D. / Xiao, B. #1: Journal: Biopolymers / Year: 1992 Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol Authors: Smith, G.D. / Dodson, G.G. #2: Journal: Nature / Year: 1989 Title: Phenol Stabilizes More Helix in a New Symmetrical Zinc Insulin Hexamer Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D. #3: Journal: Daresbury Lab.[Rep.]Dl/Sci/R / Year: 1985 Title: Molecular Replacement: The Method and its Problems (in: Molecular Replacement. Proceedings of the Daresbury Study Weekend, 15-16 February, 1985. Compiled by P.A.Machin) Authors: Dodson, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1znj.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1znj.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 1znj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/1znj ftp://data.pdbj.org/pub/pdb/validation_reports/zn/1znj | HTTPS FTP |
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-Related structure data
Related structure data | 4insS 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
-Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: HEXAMER IN ASYMMETRIC UNIT, MONOCLINIC CRYSTAL FORM 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.: 6 Source method: isolated from a genetically manipulated source Details: HEXAMER IN ASYMMETRIC UNIT, MONOCLINIC CRYSTAL FORM Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 342 molecules
#3: Chemical | ChemComp-IPH / #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: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Method: batch method / pH: 7.44 Details: BATCH, 1.7MG/ML INSULIN, 0.02 ZINC ACETATE, 0.7% (V/V) PHENOL, 0.34M SODIUM CHLORIDE, pH 7.44, batch method |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 22429 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.3 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZINC INSULIN DIMER (PDB ENTRY 4INS) Resolution: 2→8 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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