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Yorodumi- PDB-1qiy: HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED ... -
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-Basic information
Entry | Database: PDB / ID: 1qiy | ||||||
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Title | HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH PHENOL | ||||||
Components |
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Keywords | HORMONE / GLUCOSE METABOLISM / DIABETES / INSULIN MUTANT | ||||||
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: 2.3 Å | ||||||
Authors | Tang, L. / Whittingham, J.L. / Verma, C.S. / Caves, L.S.D. / Dodson, G.G. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural Consequences of the B5 Histidine --> Tyrosine Mutation in Human Insulin Characterized by X-Ray Crystallography and Conformational Analysis. Authors: Tang, L. / Whittingham, J.L. / Verma, C.S. / Caves, L.S.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 | 1qiy.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qiy.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qiy ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qiy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS A 2ZN INSULIN HEXAMER,CONSISTING OF THREE EQUIVALENT DIMERS RELATED BY A NON-CRYSTALLOGRAPHIC 3-FOLD SYMMETRY AXIS. THE ZINC AND CHLORIDE IONS ARE LOCATED ON THIS 3-FOLD AXIS. |
-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 Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3458.980 Da / Num. of mol.: 6 / Mutation: YES 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, 101 molecules
#3: Chemical | ChemComp-IPH / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN B, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 29 TO TYR ...ENGINEERED |
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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: 2.5 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: CRYSTALLISATION IN BATCH, 10 MG B5 TYR INSULIN DISSOLVED IN 2 ML 0.02M HCL. TO THIS ADDED 0.1 ML 0.12M ZINC ACETATE, 1.5 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 2.5% (AQ.) PHENOL AND 120 MG NACL. ...Details: CRYSTALLISATION IN BATCH, 10 MG B5 TYR INSULIN DISSOLVED IN 2 ML 0.02M HCL. TO THIS ADDED 0.1 ML 0.12M ZINC ACETATE, 1.5 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 2.5% (AQ.) PHENOL AND 120 MG NACL. PH ADJUSTED TO 6.5-7.8 . | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / PH range low: 7.8 / PH range high: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MULTIWIRE SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→36.8 Å / Num. obs: 13832 / % possible obs: 92 % / Redundancy: 1.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 5 / % possible all: 95.5 |
Reflection shell | *PLUS % possible obs: 95.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: R6 (NATIVE) INSULIN Resolution: 2.3→36.8 Å / σ(F): 0 Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, A4, A14, B13, B21, B29, B30, C4, D1, E5, F1, F21, F25, G4, H13, H21, J21, L1, L21, L30 THE FOLLOWING CHAIN ...Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, A4, A14, B13, B21, B29, B30, C4, D1, E5, F1, F21, F25, G4, H13, H21, J21, L1, L21, L30 THE FOLLOWING CHAIN TERMINAL RESIDUES HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, D29-D30, F29-F30, H29-H30, J29-J30
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Displacement parameters | Biso mean: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→36.8 Å
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Refine LS restraints |
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