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Yorodumi- PDB-2dsq: Structural Basis for the Inhibition of Insulin-like Growth Factor... -
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-Basic information
Entry | Database: PDB / ID: 2dsq | ||||||
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Title | Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins | ||||||
Components |
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Keywords | PROTEIN BINDING/HORMONE/GROWTH FACTOR / IGF / IGFBP / Insulin / PROTEIN BINDING-HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of insulin-like growth factor receptor signaling pathway / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development ...regulation of insulin-like growth factor receptor signaling pathway / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of neuroinflammatory response / negative regulation of vascular associated smooth muscle cell apoptotic process / bone mineralization involved in bone maturation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / positive regulation of cell growth involved in cardiac muscle cell development / IRS-related events triggered by IGF1R / insulin-like growth factor binding / ATF4 activates genes in response to endoplasmic reticulum stress / exocytic vesicle / tissue regeneration / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin-like growth factor II binding / type B pancreatic cell proliferation / positive regulation of transcription regulatory region DNA binding / insulin-like growth factor I binding / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of Ras protein signal transduction / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / muscle organ development / negative regulation of interleukin-1 beta production / positive regulation of cardiac muscle hypertrophy / positive regulation of activated T cell proliferation / positive regulation of smooth muscle cell migration / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / negative regulation of tumor necrosis factor production / regulation of glucose metabolic process / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of DNA binding / SHC-related events triggered by IGF1R / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of osteoblast differentiation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of epithelial cell proliferation / positive regulation of protein secretion / regulation of cell growth / positive regulation of glucose import / negative regulation of extrinsic apoptotic signaling pathway / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / growth factor activity / wound healing / insulin receptor binding / negative regulation of canonical Wnt signaling pathway / response to organic cyclic compound / hormone activity / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / insulin receptor signaling pathway / response to heat / positive regulation of cell growth / regulation of gene expression / cell population proliferation / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein stabilization / positive regulation of cell migration / endoplasmic reticulum lumen / negative regulation of gene expression / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sitar, T. / Popowicz, G.M. / Siwanowicz, I. / Huber, R. / Holak, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins. Authors: Sitar, T. / Popowicz, G.M. / Siwanowicz, I. / Huber, R. / Holak, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dsq.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dsq.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/2dsq ftp://data.pdbj.org/pub/pdb/validation_reports/ds/2dsq | HTTPS FTP |
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-Related structure data
Related structure data | 2dspSC 2dsrC S: Starting model for refinement C: citing same article (ref.) |
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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 | Mass: 9826.498 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P22692 #2: Protein | Mass: 7663.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P05019, UniProt: Q9NP10*PLUS #3: Protein | Mass: 10878.295 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P08833 |
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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: 2.22 Å3/Da / Density % sol: 44.67 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 22, 2006 / Details: monochromator |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 14042 / Num. obs: 13980 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DSP Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.792 / SU B: 25.25 / SU ML: 0.506 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.922 / ESU R Free: 0.522 / 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: 59.895 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.867 Å / Total num. of bins used: 20
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