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Yorodumi- PDB-4xss: Insulin-like growth factor I in complex with site 1 of a hybrid i... -
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-Basic information
Entry | Database: PDB / ID: 4xss | |||||||||
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Title | Insulin-like growth factor I in complex with site 1 of a hybrid insulin receptor / Type 1 insulin-like growth factor receptor | |||||||||
Components |
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Keywords | Hormone/hormone receptor / CELL SURFACE RECEPTOR/IMMUNE SYSTEM / INSULIN RECEPTOR / CT PEPTIDE / INSULIN-LIKE GROWTH FACTOR RECEPTOR / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM COMPLEX / Hormone-hormone receptor complex | |||||||||
Function / homology | Function and homology information 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 / cardiac atrium development / proteoglycan biosynthetic process / negative regulation of cholangiocyte apoptotic process / positive regulation of glycoprotein biosynthetic process ...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 / cardiac atrium development / proteoglycan biosynthetic process / negative regulation of cholangiocyte apoptotic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / 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 / insulin-like growth factor binding / protein transporter activity / exocytic vesicle / regulation of female gonad development / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of meiotic cell cycle / positive regulation of DNA metabolic process / positive regulation of transcription regulatory region DNA binding / cellular response to zinc ion starvation / cellular response to aldosterone / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / exocrine pancreas development / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / positive regulation of Ras protein signal transduction / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / cargo receptor activity / muscle organ development / negative regulation of interleukin-1 beta production / dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / insulin binding / response to L-glutamate / PTB domain binding / adrenal gland development / negative regulation of MAPK cascade / establishment of cell polarity / positive regulation of DNA binding / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / neuronal cell body membrane / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of activated T cell proliferation / negative regulation of release of cytochrome c from mitochondria / positive regulation of osteoblast proliferation / positive regulation of respiratory burst / positive regulation of cytokinesis / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of receptor internalization / regulation of embryonic development / regulation of JNK cascade / negative regulation of tumor necrosis factor production / insulin receptor substrate binding / transport across blood-brain barrier / estrous cycle / positive regulation of glycogen biosynthetic process / G-protein alpha-subunit binding / response to vitamin E / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / epithelial to mesenchymal transition / SHC-related events triggered by IGF1R / Signal attenuation / positive regulation of osteoblast differentiation / phosphatidylinositol 3-kinase binding / heart morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of tyrosine phosphorylation of STAT protein Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Lawrence, C. / Kong, G.K.-W. / Menting, J.G. / Lawrence, M.C. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Structure / Year: 2015 Title: Structural Congruency of Ligand Binding to the Insulin and Insulin/Type 1 Insulin-like Growth Factor Hybrid Receptors. Authors: Menting, J.G. / Lawrence, C.F. / Kong, G.K. / Margetts, M.B. / Ward, C.W. / Lawrence, M.C. #1: Journal: PROC.NATL.ACAD.SCI.USA / Year: 2014 Title: PROTECTIVE HINGE IN INSULIN OPENS TO ENABLE ITS RECEPTOR ENGAGEMENT Authors: Menting, J.G. #2: Journal: Nature / Year: 2013 Title: How insulin engages its primary binding site on the insulin receptor Authors: Menting, J.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xss.cif.gz | 175.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xss.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 4xss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/4xss ftp://data.pdbj.org/pub/pdb/validation_reports/xs/4xss | HTTPS FTP |
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-Related structure data
Related structure data | 4xstC 3loh 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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2 |
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Unit cell |
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-Components
-Insulin-like growth factor ... , 2 types, 2 molecules BF
#1: Protein | Mass: 7663.752 Da / Num. of mol.: 1 / Fragment: UNP residues 49-118 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1, IBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05019 |
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#3: Protein/peptide | Mass: 1947.195 Da / Num. of mol.: 1 / Fragment: Alpha-CT peptide, UNP residues 691-706 / Source method: obtained synthetically / Details: Chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P08069*PLUS |
-Protein / Non-polymers , 2 types, 2 molecules E
#2: Protein | Mass: 36231.762 Da / Num. of mol.: 1 / Fragment: L1-CR, UNP residues 28-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): LEC 8 MUTANT CHO CELL / Production host: Cricetulus Griseus (Chinese hamster) References: UniProt: P06213, receptor protein-tyrosine kinase |
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#6: Chemical | ChemComp-SO4 / |
-Sugars , 3 types, 6 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#7: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.11 Å3/Da / Density % sol: 79.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 1.75 M ammonium sulfate, 0.1 M CAPS-NaOH (pH 10.5), 0.2 M LiSO4 |
-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 315 / Detector: CCD / Date: Feb 17, 2013 |
Radiation | Monochromator: Double crystal monochromator (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.28 Å / Num. obs: 22377 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 92.17 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 6.2 % / Rmerge F obs: 0.696 / Rmerge(I) obs: 2.11 / Mean I/σ(I) obs: 0.9 / Num. measured obs: 23716 / Num. possible: 2068 / Num. unique obs: 2068 / Rrim(I) all: 2.209 / Rejects: 0 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LOH 3loh Resolution: 3→48.28 Å / Cor.coef. Fo:Fc: 0.9254 / Cor.coef. Fo:Fc free: 0.9127 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.332 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.254
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Displacement parameters | Biso mean: 129.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.721 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.15 Å / Total num. of bins used: 11
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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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