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Yorodumi- PDB-5u8r: Structure of the ectodomain of the human Type 1 insulin-like grow... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u8r | |||||||||||||||
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Title | Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor | |||||||||||||||
Components |
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Keywords | TRANSFERASE/IMMUNE SYSTEM / Receptor / tyrosine kinase / Type 1 insulin-like / growth factor receptor / TRANSFERASE-IMMUNE SYSTEM complex | |||||||||||||||
Function / homology | Function and homology information cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / insulin receptor complex / negative regulation of hepatocyte apoptotic process / cellular response to testosterone stimulus / insulin-like growth factor I binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / positive regulation of protein-containing complex disassembly / cellular response to angiotensin / cellular response to insulin-like growth factor stimulus / response to L-glutamate / dendritic spine maintenance / insulin binding / establishment of cell polarity / negative regulation of MAPK cascade / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / regulation of JNK cascade / estrous cycle / insulin receptor substrate binding / G-protein alpha-subunit binding / response to vitamin E / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / cerebellum development / cellular response to dexamethasone stimulus / axonogenesis / insulin-like growth factor receptor signaling pathway / response to nicotine / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / caveola / hippocampus development / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / receptor protein-tyrosine kinase / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein tyrosine kinase activity / response to ethanol / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00001618041 Å | |||||||||||||||
Authors | Lawrence, M. / Xu, Y. | |||||||||||||||
Funding support | Australia, 4items
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Citation | Journal: Nat Commun / Year: 2018 Title: 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. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u8r.cif.gz | 523.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u8r.ent.gz | 365.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/5u8r ftp://data.pdbj.org/pub/pdb/validation_reports/u8/5u8r | HTTPS FTP |
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-Related structure data
Related structure data | 5u8qC 1igrS 3umtS 4zxbS C: citing same article (ref.) 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 | Assembly determined by non-denaturing gel |
-Components
-Protein , 1 types, 1 molecules A
#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.ECD Details (production host): see Whitten et al., J. Mol. Biol., v394, pp878-92 (2009). Cell line (production host): Lec8 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P08069, receptor protein-tyrosine kinase |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 13948.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pgpHFT-SUMO-scFV / Production host: Spodoptera frugiperda (fall armyworm) |
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#3: Antibody | Mass: 11733.944 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pgpHFT-SUMO-scFV / Production host: Spodoptera frugiperda (fall armyworm) |
-Sugars , 2 types, 6 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 4 molecules
#5: Chemical | ChemComp-SO4 / | ||
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#6: Chemical | #8: Chemical | ChemComp-IMD / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.4 % |
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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 |
-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: Oct 21, 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→50 Å / Num. obs: 45844 / % possible obs: 99.7 % / Redundancy: 8.9 % / Biso Wilson estimate: 92.4253334113 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.25 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3→3.13 Å / Redundancy: 7.2 % / Rmerge(I) obs: 3.47 / Mean I/σ(I) obs: 0.6 / Num. unique all: 5400 / CC1/2: 0.551 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: domains from 1IGR, 4ZXB, 3UMT Resolution: 3.00001618041→46.3593115758 Å / SU ML: 0.559199999756 / Cross valid method: FREE R-VALUE / σ(F): 1.33687173502 / Phase error: 37.3303485675 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: 133.915230855 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.00001618041→46.3593115758 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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