+Open data
-Basic information
Entry | Database: PDB / ID: 3q6e | ||||||
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Title | Human insulin in complex with cucurbit[7]uril | ||||||
Components |
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Keywords | HORMONE / INSULIN / CUCURBIT[7]URIL / CUCURBITURIL / SYNTHETIC / HOST / PHENYLALANINE / SUPRAMOLECULAR / RECOGNITION / CARBOHYDRATE METABOLISM / CLEAVAGE ON PAIR OF BASIC RESIDUES / DIABETES MELLITUS / DISEASE MUTATION / DISULFIDE BOND / GLUCOSE METABOLISM / SECRETED | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Chinai, J.M. / Taylor, A.B. / Hargreaves, N.D. / Ryno, L.M. / Morris, C.A. / Hart, P.J. / Urbach, A.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Molecular recognition of insulin by a synthetic receptor. Authors: Chinai, J.M. / Taylor, A.B. / Ryno, L.M. / Hargreaves, N.D. / Morris, C.A. / Hart, P.J. / Urbach, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q6e.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q6e.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 3q6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q6e ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q6e | HTTPS FTP |
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-Related structure data
Related structure data | 1msoS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: unp residues 90-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: unp residues 25-54 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01308 #3: Chemical | ChemComp-QQ7 / | #4: 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: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: 40 uM Q7, 40 uM insulin, 10 mM sodium phosphate, 4 mM EDTA, 1 mM lysine, EVAPORATION, temperature 298K, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 / Wavelength: 0.97947 Å | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2008 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SINGLE CRYSTAL SIDE-BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→30 Å / Num. obs: 8778 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 35.7 | |||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.521 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSO Resolution: 2.05→27.47 Å / SU ML: 0.31 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.33 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→27.47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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