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Yorodumi- PDB-3e50: Crystal structure of human insulin degrading enzyme in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 3.0E+50 | ||||||
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Title | Crystal structure of human insulin degrading enzyme in complex with transforming growth factor-alpha | ||||||
Components |
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Keywords | Hydrolase/Hormone / IDE / TGF-ALPHA / Cytoplasm / Hydrolase / Metal-binding / Metalloprotease / Polymorphism / Protease / Zinc / Cell membrane / EGF-like domain / Glycoprotein / Growth factor / Lipoprotein / Membrane / Mitogen / Palmitate / Secreted / Transmembrane / Hydrolase-Hormone COMPLEX | ||||||
Function / homology | Function and homology information insulysin / hepatocyte proliferation / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / Cargo concentration in the ER / ubiquitin-modified protein reader activity ...insulysin / hepatocyte proliferation / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / Cargo concentration in the ER / ubiquitin-modified protein reader activity / Inhibition of Signaling by Overexpressed EGFR / COPII-mediated vesicle transport / EGFR interacts with phospholipase C-gamma / insulin binding / ERBB2-EGFR signaling pathway / regulation of aerobic respiration / epidermal growth factor receptor binding / Signaling by EGFR / peptide catabolic process / transmembrane receptor protein tyrosine kinase activator activity / amyloid-beta clearance / peroxisomal matrix / positive regulation of cell division / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / GAB1 signalosome / amyloid-beta metabolic process / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Insulin receptor recycling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / endoplasmic reticulum-Golgi intermediate compartment membrane / proteolysis involved in protein catabolic process / positive regulation of mitotic nuclear division / positive regulation of epithelial cell proliferation / Peroxisomal protein import / peptide binding / EGFR downregulation / protein catabolic process / growth factor activity / clathrin-coated endocytic vesicle membrane / epidermal growth factor receptor signaling pathway / ER to Golgi transport vesicle membrane / metalloendopeptidase activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / peroxisome / positive regulation of protein catabolic process / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / PIP3 activates AKT signaling / insulin receptor signaling pathway / Clathrin-mediated endocytosis / positive regulation of protein binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / endopeptidase activity / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / receptor ligand activity / Ub-specific processing proteases / intracellular signal transduction / external side of plasma membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Guo, Q. / Manolopoulou, M. / Tang, W.-J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-alpha, and Amylin by Human Insulin-Degrading Enzyme. Authors: Guo, Q. / Manolopoulou, M. / Bian, Y. / Schilling, A.B. / Tang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e50.cif.gz | 414.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e50.ent.gz | 328.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/3e50 ftp://data.pdbj.org/pub/pdb/validation_reports/e5/3e50 | HTTPS FTP |
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-Related 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 | Mass: 114715.141 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019 / Mutation: E111Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_1810909, IDE, RP11-366I13.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin #2: Protein/peptide | Mass: 5560.246 Da / Num. of mol.: 2 Fragment: UNP residues 40-89, Transforming growth factor alpha chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFA / References: UniProt: P01135 #3: Chemical | #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: 3.73 Å3/Da / Density % sol: 67.05 % |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0003 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0003 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 159824 / Num. obs: 157230 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.087 / Net I/σ(I): 23.6 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.982 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.179 / 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: 32.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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