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Yorodumi- PDB-3h44: Crystal Structure of Insulin Degrading Enzyme in Complex with mac... -
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-Basic information
Entry | Database: PDB / ID: 3h44 | ||||||
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Title | Crystal Structure of Insulin Degrading Enzyme in Complex with macrophage inflammatory protein 1 alpha | ||||||
Components |
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Keywords | Hydrolase/Cytokine / IDE / MIP1alpha / Cytoplasm / Hydrolase / Metal-binding / Metalloprotease / Polymorphism / Protease / Zinc / Chemotaxis / Cytokine / Disulfide bond / Inflammatory response / Secreted / Hydrolase-Cytokine COMPLEX | ||||||
Function / homology | Function and homology information granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / insulysin / signaling / ubiquitin recycling / astrocyte cell migration / eosinophil degranulation ...granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / insulysin / signaling / ubiquitin recycling / astrocyte cell migration / eosinophil degranulation / insulin catabolic process / insulin metabolic process / CCR5 chemokine receptor binding / negative regulation of bone mineralization / regulation of sensory perception of pain / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / amyloid-beta clearance by cellular catabolic process / cell activation / hormone catabolic process / bradykinin catabolic process / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration / phospholipase activator activity / peptide catabolic process / macrophage chemotaxis / amyloid-beta clearance / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / peroxisomal matrix / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / amyloid-beta metabolic process / cytoskeleton organization / Insulin receptor recycling / proteolysis involved in protein catabolic process / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / Peroxisomal protein import / peptide binding / protein catabolic process / intracellular calcium ion homeostasis / metalloendopeptidase activity / response to toxic substance / antigen processing and presentation of endogenous peptide antigen via MHC class I / osteoblast differentiation / positive regulation of inflammatory response / peroxisome / cellular response to type II interferon / positive regulation of protein catabolic process / positive regulation of neuron apoptotic process / calcium ion transport / chemotaxis / MAPK cascade / positive regulation of tumor necrosis factor production / virus receptor activity / cell-cell signaling / insulin receptor signaling pathway / cellular response to tumor necrosis factor / positive regulation of protein binding / kinase activity / regulation of cell shape / basolateral plasma membrane / endopeptidase activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Ub-specific processing proteases / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ren, M. / Guo, Q. / Tang, W.J. | ||||||
Citation | Journal: To be Published Title: Macrophage Inflammatory Protein-1 Is A Novel High Affinity Substrate For Human Insulin Degrading Enzyme Authors: Ren, M. / Guo, Q. / 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 | 3h44.cif.gz | 406.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h44.ent.gz | 319.5 KB | Display | PDB format |
PDBx/mmJSON format | 3h44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/3h44 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/3h44 | HTTPS FTP |
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-Related structure data
Related structure data | 2wbyS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 114560.578 Da / Num. of mol.: 2 / Fragment: residues 42-1019 Mutation: C110L, E111Q, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDE / Plasmid: proEX-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P14735, insulysin #2: Protein | Mass: 7793.664 Da / Num. of mol.: 2 / Fragment: residues 23-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCL3, G0S19-1, MIP1A, MIP1alpha, SCYA3 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10147 #3: Chemical | ChemComp-DIO / #4: Chemical | #5: 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: 3.68 Å3/Da / Density % sol: 66.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13% PEGMME 5000, 100mM HEPES, pH 7.0, 10%, Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008 / Details: bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 67989 / Num. obs: 67744 / % possible obs: 99.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / Rsym value: 0.514 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2wby Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.005 / SU ML: 0.249 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 1.096 / ESU R Free: 0.351 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.95 Å2
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Total num. of bins used: 20
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