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Yorodumi- PDB-1trz: CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1trz | ||||||
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Title | CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE | ||||||
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 / Resolution: 1.6 Å | ||||||
Authors | Ciszak, E. / Smith, G.D. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Crystallographic evidence for dual coordination around zinc in the T3R3 human insulin hexamer. Authors: Ciszak, E. / Smith, G.D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984 Title: Structural Stability in the 4-Zinc Human Insulin Hexamer Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. #2: Journal: Nature / Year: 1976 Title: Structure of Insulin in 4-Zinc Insulin Authors: Bentley, G. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D. / Mercola, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1trz.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1trz.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1trz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/1trz ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1trz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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8 |
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9 |
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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 / Source method: obtained synthetically / Details: Crystalline biosynthetic human insulin / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Crystalline biosynthetic human insulin / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 128 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | THE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION OF THE ...THE CONFORMATI |
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Nonpolymer details | EACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED B 10 HIS. THE COORDINATION ...EACH OF TWO ZINC IONS IS COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.45 % / Description: Colorless, sharp-edged rhombohedrons up to 1mm | ||||||||||||||||||||||||
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Crystal grow | pH: 6.4 Details: Crystals were grown from 0.05M sodium citrate and 0.007M zinc acetate in the presence of 0.75M sodium chloride at pH6.4 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.541 / Wavelength: 1.541 Å |
Detector | Detector: IMAGE PLATE |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Rmerge(I) obs: 0.054 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 11601 / Num. measured all: 34613 / Rmerge(I) obs: 0.054 |
-Processing
Software | Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.6→8 Å Details: SIDE CHAINS OF VAL D 2 (MON II), LYS B 29 AND THR B 30 OF BOTH MONOMERS ARE NOT INCLUDED IN THE MODEL. THE SIDE CHAINS OF B 109 AND B 105 ARE REFINED IN TWO ALTERNATE ORIENTATIONS.
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 9225 / σ(F): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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