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Yorodumi- PDB-5u8q: Structure of the ectodomain of the human Type 1 insulin-like grow... -
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Basic information
| Entry | Database: PDB / ID: 5u8q | |||||||||
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| Title | Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor in complex with IGF-I | |||||||||
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Keywords | TRANSFERASE / Receptor tyrosine kinase / Type 1 insulin-like growth factor receptor / insulin-like growth-factor I | |||||||||
| Function / homology | Function and homology informationglycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process / type II pneumocyte differentiation ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process / type II pneumocyte differentiation / neuronal dense core vesicle lumen / proteoglycan biosynthetic process / regulation of establishment or maintenance of cell polarity / chondroitin sulfate proteoglycan biosynthetic process / protein kinase complex / insulin-like growth factor receptor activity / myotube cell development / positive regulation of transcription regulatory region DNA binding / negative regulation of neuroinflammatory response / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / protein transporter activity / bone mineralization involved in bone maturation / positive regulation of cell growth involved in cardiac muscle cell development / IRS-related events triggered by IGF1R / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of cerebellar granule cell precursor proliferation / lung vasculature development / exocytic vesicle / transcytosis / cerebellar granule cell precursor proliferation / positive regulation of myoblast proliferation / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / cell activation / glial cell differentiation / positive regulation of calcineurin-NFAT signaling cascade / prostate gland growth / transmembrane receptor protein tyrosine kinase activator activity / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / type B pancreatic cell proliferation / insulin receptor activity / mammary gland development / exocrine pancreas development / alphav-beta3 integrin-IGF-1-IGF1R complex / myoblast differentiation / cell surface receptor signaling pathway via STAT / regulation of nitric oxide biosynthetic process / positive regulation of Ras protein signal transduction / positive regulation of insulin-like growth factor receptor signaling pathway / dendritic spine maintenance / regulation of JNK cascade / peptidyl-tyrosine autophosphorylation / positive regulation of smooth muscle cell migration / growth hormone receptor signaling pathway / insulin binding / positive regulation of DNA binding / negative regulation of interleukin-1 beta production / lung alveolus development / muscle organ development / cellular response to insulin-like growth factor stimulus / branching morphogenesis of an epithelial tube / positive regulation of cardiac muscle hypertrophy / androgen receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / negative regulation of release of cytochrome c from mitochondria / type I pneumocyte differentiation / negative regulation of smooth muscle cell apoptotic process / inner ear development / negative regulation of amyloid-beta formation / amyloid-beta clearance / positive regulation of activated T cell proliferation / Respiratory syncytial virus (RSV) attachment and entry / myoblast proliferation / insulin receptor substrate binding / epithelial to mesenchymal transition / negative regulation of tumor necrosis factor production / Synthesis, secretion, and deacylation of Ghrelin / blood vessel remodeling / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / postsynaptic modulation of chemical synaptic transmission / phosphatidylinositol 3-kinase binding / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of MAPK cascade / insulin-like growth factor receptor binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smooth muscle cell proliferation / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / positive regulation of glycolytic process / positive regulation of epithelial cell proliferation / skeletal system development Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human)![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27104018461 Å | |||||||||
Authors | Lawrence, M. / Xu, Y. | |||||||||
Citation | Journal: Nat Commun / Year: 2018Title: How ligand binds to the type 1 insulin-like growth factor receptor. Authors: Xu, Y. / Kong, G.K. / Menting, J.G. / Margetts, M.B. / Delaine, C.A. / Jenkin, L.M. / Kiselyov, V.V. / De Meyts, P. / Forbes, B.E. / Lawrence, M.C. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5u8q.cif.gz | 551 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5u8q.ent.gz | 384.2 KB | Display | PDB format |
| PDBx/mmJSON format | 5u8q.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5u8q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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| Full document | 5u8q_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | 5u8q_validation.xml.gz | 39.2 KB | Display | |
| Data in CIF | 5u8q_validation.cif.gz | 52.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/5u8q ftp://data.pdbj.org/pub/pdb/validation_reports/u8/5u8q | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5u8rSC S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| Unit cell |
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Components
-Insulin-like growth factor ... , 2 types, 2 molecules AB
| #1: Protein | Mass: 101085.461 Da / Num. of mol.: 1 Mutation: residues 718-741 are replaced with the sequence AGNN Source method: isolated from a genetically manipulated source Details: A17delta-beta construct, see Whitten et al., J. Mol. Biol., v394, pp878-92 (2009). Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Plasmid: FIII-IGFR.ECDDetails (production host): see Whitten et al., J. Mol. Biol., v394, pp878-92 (2009). Cell line (production host): Lec8 / Production host: ![]() References: UniProt: P08069, receptor protein-tyrosine kinase |
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| #2: Protein | Mass: 7663.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mature IGF-1 / Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1, IBP1 / Production host: ![]() |
-Antibody , 2 types, 2 molecules HL
| #3: Antibody | Mass: 13948.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) ![]() ![]() |
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| #4: Antibody | Mass: 11733.944 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) ![]() ![]() |
-Sugars , 3 types, 6 molecules 
| #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | |
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-Non-polymers , 2 types, 3 molecules 


| #7: Chemical | | #8: Chemical | ChemComp-MLT / | |
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-Details
| Has protein modification | Y |
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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: 3.84 Å3/Da / Density % sol: 67.94 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 M ammonium sulfate, 0.1 M imidazole-malate pH 7.0. IGF-1 was included by soaking directly into the mother crystal. For full details see the primary citation. |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
| Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2016 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
| Reflection | Resolution: 3.27→50 Å / Num. obs: 32228 / % possible obs: 98.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 110.958573147 Å2 / CC1/2: 0.775 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.1 |
| Reflection shell | Resolution: 3.27→3.46 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4896 / CC1/2: 0.775 / % possible all: 92.5 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 5U8R Resolution: 3.27104018461→22.1725 Å / SU ML: 0.543083052018 / Cross valid method: FREE R-VALUE / σ(F): 1.32594454353 / Phase error: 38.9050389519 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 177.857907853 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.27104018461→22.1725 Å
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Homo sapiens (human)
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