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Yorodumi- PDB-1qiz: HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qiz | ||||||
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Title | HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH RESORCINOL | ||||||
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 / 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 ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 respiratory burst / positive regulation of peptide hormone secretion / 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 / 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 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic 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 / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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 | 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 | 1qiz.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qiz.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qiz_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 1qiz_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 1qiz_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 1qiz_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qiz ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qiz | HTTPS FTP |
-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 ANDCHLORIDE 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 / 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 #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, 169 molecules
#3: Chemical | ChemComp-RCO / #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: 2.5 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, 1.04 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 5.0% (AQ.) PHENOL AND 120 MG ...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, 1.04 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 5.0% (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: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 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→19.2 Å / Num. obs: 21525 / % possible obs: 96 % / Redundancy: 2.5 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3 / % possible all: 87.6 |
Reflection shell | *PLUS % possible obs: 87.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: R6 (NATIVE) INSULIN Resolution: 2→19.2 Å / σ(F): 0 Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER: A4, A5, A14, A18, B21, B25, D1, D3, D21, E5, F1, F21, F25, F29, G4, H4, H13, H29, I14, J29, K4, K14, L1, L21, ...Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER: A4, A5, A14, A18, B21, B25, D1, D3, D21, E5, F1, F21, F25, F29, G4, H4, H13, H29, I14, J29, K4, K14, L1, L21, L29 THE FOLLOWING CHAIN TERMINAL RESIDUES HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER: B30, D29-D30, F30, H30, J30, L30
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.2 Å
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Refine LS restraints |
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