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Yorodumi- PDB-1wqj: Structural Basis for the Regulation of Insulin-Like Growth Factor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wqj | ||||||
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Title | Structural Basis for the Regulation of Insulin-Like Growth Factors (IGFs) by IGF Binding Proteins (IGFBPs) | ||||||
Components |
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Keywords | PROTEIN BINDING/HORMONE/GROWTH FACTOR / PROTEIN-PROTEIN COMPLEX / DISULFIDE RICH / DISULFIDE BOND LADDER / 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 / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of vascular associated smooth muscle cell apoptotic process / bone mineralization involved in bone maturation / IRS-related events triggered by IGF1R / exocytic vesicle / positive regulation of transcription regulatory region DNA binding / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin-like growth factor II binding / type B pancreatic cell proliferation / 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 DNA binding / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / 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 / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / positive regulation of epithelial cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / activation of protein kinase B activity / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of smooth muscle cell proliferation / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of glucose import / positive regulation of protein secretion / regulation of cell growth / Post-translational protein phosphorylation / regulation of protein phosphorylation / insulin receptor binding / growth factor activity / wound healing / negative regulation of canonical Wnt signaling pathway / hormone activity / response to organic cyclic compound / positive regulation of fibroblast proliferation / integrin binding / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / MAPK cascade / Platelet degranulation / regulation of gene expression / response to heat / Ras protein signal transduction / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Siwanowicz, I. / Popowicz, G.M. / Wisniewska, M. / Huber, R. / Kuenkele, K.P. / Lang, K. / Engh, R.A. / Holak, T.A. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Structural basis for the regulation of insulin-like growth factors by IGF binding proteins Authors: Siwanowicz, I. / Popowicz, G.M. / Wisniewska, M. / Huber, R. / Kuenkele, K.P. / Lang, K. / Engh, R.A. / 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 | 1wqj.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wqj.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wqj_validation.pdf.gz | 431.4 KB | Display | wwPDB validaton report |
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Full document | 1wqj_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 1wqj_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1wqj_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/1wqj ftp://data.pdbj.org/pub/pdb/validation_reports/wq/1wqj | HTTPS FTP |
-Related structure data
Related structure data | 1h59S 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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Unit cell |
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Details | 1:1 (B:I) stechiometry binary complex, single complex molecule per assymetric unit |
-Components
#1: Protein | Mass: 8498.120 Da / Num. of mol.: 1 / Fragment: NBP-4 (residues 3-82) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22692 |
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#2: Protein | Mass: 7663.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P05019 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 23% PEG 1500, 25mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2003 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37 Å / Num. all: 86002 / Num. obs: 17605 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.044 / Rsym value: 0.04 / Net I/σ(I): 16.86 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5.45 / Num. unique all: 1964 / Rsym value: 0.144 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H59 Resolution: 1.6→31.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.851 / SU ML: 0.065 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.126 / ESU R Free: 0.11 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→31.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20 /
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