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Basic information
Entry | Database: PDB / ID: 1gzr | |||||||||
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Title | Human Insulin-like growth factor; ESRF data | |||||||||
![]() | INSULIN-LIKE GROWTH FACTOR I | |||||||||
![]() | GROWTH FACTOR / INSULIN FAMILY / IGF-1 / PLASMA | |||||||||
Function / homology | ![]() 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 ...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 / 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 / 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 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 / insulin-like growth factor receptor signaling pathway / positive regulation of epithelial cell proliferation / platelet alpha granule lumen / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of glucose import / positive regulation of protein secretion / positive regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / insulin receptor binding / growth factor activity / wound healing / 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) / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / Ras protein signal transduction / cell population proliferation / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Brzozowski, A.M. / Dodson, E.J. / Dodson, G.G. / Murshudov, G. / Verma, C. / Turkenburg, J.P. / De Bree, F.M. / Dauter, Z. | |||||||||
![]() | ![]() Title: Structural Origins of the Functional Divergence of Human Insulin-Like Growth Factor-I and Insulin Authors: Brzozowski, A.M. / Dodson, E.J. / Dodson, G.G. / Murshudov, G. / Verma, C. / Turkenburg, J.P. / De Bree, F.M. / Dauter, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 27 KB | Display | ![]() |
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PDB format | ![]() | 16.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gzyC ![]() 1gzzC ![]() 1h02C ![]() 4insS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7663.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-C15 / |
#3: Water | ChemComp-HOH / |
Compound details | INSULIN-LIKE GROWTH FACTORS,ARE FUNCTIONALLY AND STRUCTURALLY RELATED TO INSULIN WITH HIGHER GROWTH- ...INSULIN-LIKE GROWTH FACTORS,ARE FUNCTIONAL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7. ...Details: THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD IN WHICH DROPS WERE COMPOSED OF VARIOUS RATIOS OF HIGF-I AT 7MG/ML (IN H2O) WITH RESERVOIR SOLUTION CONSISTING OF 0.1M TRIS.HCL PH 7.5, 12-15% (W/V) PEG 2K AND 5MM SB12 DETERGENT. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 4839 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 12 / % possible all: 95.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 17172 |
Reflection shell | *PLUS % possible obs: 95.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB EBTRY 4INS Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.553 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 27.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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