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Yorodumi- PDB-2wc0: crystal structure of human insulin degrading enzyme in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 2wc0 | ||||||
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Title | crystal structure of human insulin degrading enzyme in complex with iodinated insulin | ||||||
Components |
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Keywords | HYDROLASE/HORMONE / ZINC / DIOXANE / INSULIN / HORMONE / PROTEASE / SECRETED / HUMAN INSULIN-DEGRADING ENZYME / DISULFIDE BOND / METALLOPROTEASE / GLUCOSE METABOLISM / CARBOHYDRATE METABOLISM / HYDROLASE / CYTOPLASM / POLYMORPHISM / METAL-BINDING / CLEAVAGE ON PAIR OF BASIC RESIDUES / HYDROLASE-HORMONE complex | ||||||
Function / homology | Function and homology information insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of aerobic respiration / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / peptide catabolic process / IRS activation / Insulin processing / regulation of protein secretion / amyloid-beta clearance / 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 / peroxisomal matrix / regulation of cellular amino acid metabolic process / 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 / amyloid-beta metabolic process / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / peptide binding / proteolysis involved in protein catabolic process / 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 / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / Peroxisomal protein import / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / protein catabolic process / regulation of synaptic plasticity / vasodilation / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / positive regulation of protein catabolic process / glucose metabolic process / regulation of protein localization / glucose homeostasis / virus receptor activity / positive regulation of protein binding / insulin receptor signaling pathway / cell-cell signaling / peroxisome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / basolateral plasma membrane / endopeptidase activity / protease binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Manolopoulou, M. / Guo, Q. / Malito, E. / Schilling, A.B. / Tang, W.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Molecular Basis of Catalytic Chamber-Assisted Unfolding and Cleavage of Human Insulin by Human Insulin Degrading Enzyme. Authors: Manolopoulou, M. / Guo, Q. / Malito, E. / Schilling, A.B. / Tang, W.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wc0.cif.gz | 425.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wc0.ent.gz | 336.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wc0_validation.pdf.gz | 514.4 KB | Display | wwPDB validaton report |
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Full document | 2wc0_full_validation.pdf.gz | 597.9 KB | Display | |
Data in XML | 2wc0_validation.xml.gz | 81.4 KB | Display | |
Data in CIF | 2wc0_validation.cif.gz | 109.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/2wc0 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/2wc0 | HTTPS FTP |
-Related structure data
Related structure data | 2wbyC 2g47S C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 114560.578 Da / Num. of mol.: 2 / Fragment: RESIDUES 42-1019 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14735, insulysin |
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-Protein/peptide , 2 types, 4 molecules CEDF
#2: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: RESIDUES 90-110 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #3: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-54 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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-Non-polymers , 3 types, 370 molecules
#4: Chemical | #5: Chemical | ChemComp-DIO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 110 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLU 111 TO GLN ...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: 3.87 Å3/Da / Density % sol: 67.93 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.548 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.548 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 97980 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.6 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G47 Resolution: 2.8→29.85 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.117 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.471 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.85 Å
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