+Open data
-Basic information
Entry | Database: PDB / ID: 1qj0 | ||||||
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Title | HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR | ||||||
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 / 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 peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic 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 peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / positive regulation of insulin receptor signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / nitric oxide-cGMP-mediated signaling / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / transport vesicle / Insulin receptor recycling / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / acute-phase response / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / cognition / Regulation of insulin secretion / endosome lumen / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / negative regulation of protein catabolic process / regulation of synaptic plasticity / hormone activity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 1qj0.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qj0.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qj0_validation.pdf.gz | 394.9 KB | Display | wwPDB validaton report |
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Full document | 1qj0_full_validation.pdf.gz | 400.3 KB | Display | |
Data in XML | 1qj0_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 1qj0_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qj0 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qj0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | THE ASYMMETRIC UNIT CONTAINS AN INSULIN DIMER. THREE DIMERS AGGREGATE AROUND TWO ZINC IONS SITUATED ON A CRYSTALLOGRAPHIC3-FOLD AXIS TO FORM A HEXAMER.A MEAN DIFFERENCE IN ACCESSIBLE SURFACE AREA PER THE CHAIN IN THE COMPLEX OF 1325.5 ANGSTROM**2 |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 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.: 2 / 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 #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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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 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||
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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 0.05 ML 0.15M ZINC ACETATE, 1.0 ML 0.2 M TRI-SODIUM CITRATE, 1.0 ML ACETONE. PH ADJUSTED TO 6.4-7.1 . | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / PH range low: 7.1 / PH range high: 6.4 | ||||||||||||||||||||||||||||||||||||||||||
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 |
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: 2.4→25.7 Å / Num. obs: 3477 / % possible obs: 97 % / Redundancy: 2.5 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.132 / % possible all: 92 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T3R3 (NATIVE) INSULIN Resolution: 2.4→25.7 Å / σ(F): 0 Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER: A4, A5, A10, B3, B4, B21, B29, C14, D3, D4 THE FOLLOWING CHAIN TERMINAL RESIDUES HAVE BEEN ASSIGNED ZERO ...Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER: A4, A5, A10, B3, B4, B21, B29, C14, D3, D4 THE FOLLOWING CHAIN TERMINAL RESIDUES HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER: B1-B2, B30, D30 THE FOLLOWING A CHAIN RESIDUES HAVE BEEN ASSIGNED ZERO OR HALF OCCUPANCIES DUE TO DISORDER, RESULTING FROM THE B5 HIS TO TYR MUTATION: A7, A8, A9
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Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→25.7 Å
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Refine LS restraints |
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