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Yorodumi- PDB-5kqv: Insulin receptor ectodomain construct comprising domains L1,CR,L2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kqv | ||||||||||||
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Title | Insulin receptor ectodomain construct comprising domains L1,CR,L2, FnIII-1 and alphaCT peptide in complex with bovine insulin and FAB 83-14 (REVISED STRUCTURE) | ||||||||||||
Components |
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Keywords | Hormone/Hormone Receptor/Immune System / Cell surface receptor/immune system / insulin receptor / IR ectodomain / CT peptide / HORMONE-HORMONE RECEPTOR-IMMUNE SYSTEM COMPLEX | ||||||||||||
Function / homology | Function and homology information estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / regulation of female gonad development / positive regulation of meiotic cell cycle ...estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / regulation of female gonad development / positive regulation of meiotic cell cycle / negative regulation of appetite / response to butyrate / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / feeding behavior / response to growth hormone / positive regulation of protein-containing complex disassembly / cargo receptor activity / response to food / dendritic spine maintenance / insulin binding / PTB domain binding / adrenal gland development / positive regulation of Rho protein signal transduction / neuronal cell body membrane / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / amyloid-beta clearance / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / positive regulation of receptor internalization / regulation of embryonic development / transport across blood-brain barrier / protein secretion / insulin receptor substrate binding / positive regulation of glycogen biosynthetic process / epidermis development / Signal attenuation / negative regulation of lipid catabolic process / phosphatidylinositol 3-kinase binding / response to glucose / heart morphogenesis / dendrite membrane / Insulin receptor recycling / neuron projection maintenance / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / response to nutrient levels / receptor-mediated endocytosis / learning / caveola / positive regulation of protein secretion / positive regulation of glucose import / insulin-like growth factor receptor binding / positive regulation of MAP kinase activity / insulin receptor binding / positive regulation of insulin secretion / hormone activity / receptor internalization / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / glucose metabolic process / male gonad development / positive regulation of nitric oxide biosynthetic process / late endosome / insulin receptor signaling pathway / glucose homeostasis / amyloid-beta binding / response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / receptor complex / endosome membrane / positive regulation of cell migration / symbiont entry into host cell / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / protein domain specific binding / external side of plasma membrane / axon / protein phosphorylation / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å | ||||||||||||
Authors | Lawrence, M.C. / Smith, B.J. / Croll, T.I. | ||||||||||||
Funding support | Australia, 1items
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Citation | Journal: Nature / Year: 2013 Title: How insulin engages its primary binding site on the insulin receptor. Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / Dodson, ...Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / Dodson, G.G. / Brzozowski, A.M. / Weiss, M.A. / Ward, C.W. / Lawrence, M.C. #1: Journal: Structure / Year: 2016 Title: Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain. Authors: Croll, T.I. / Smith, B.J. / Margetts, M.B. / Whittaker, J. / Weiss, M.A. / Ward, C.W. / 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 | 5kqv.cif.gz | 864.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kqv.ent.gz | 731.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kqv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5kqv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5kqv_validation.xml.gz | 44 KB | Display | |
Data in CIF | 5kqv_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/5kqv ftp://data.pdbj.org/pub/pdb/validation_reports/kq/5kqv | HTTPS FTP |
-Related structure data
Related structure data | 3w11C 3w12C 3w13C 4zxbS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein/peptide , 2 types, 4 molecules AIBJ
#1: Protein/peptide | Mass: 2339.645 Da / Num. of mol.: 2 / Fragment: UNP Residues 85-105 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: UNP Residues 25-54 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 |
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-Protein , 1 types, 2 molecules EF
#5: Protein | Mass: 69979.859 Da / Num. of mol.: 2 / Mutation: Y144H,Y144H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Plasmid: PEE14 / Cell line (production host): Lec8 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P06213, receptor protein-tyrosine kinase |
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-Antibody , 2 types, 4 molecules CPDQ
#3: Antibody | Mass: 23622.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma #4: Antibody | Mass: 23514.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma |
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-Sugars , 2 types, 3 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: 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 | Source method: isolated from a genetically manipulated source |
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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: 3.26 Å3/Da / Density % sol: 62.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 9% POLYETHYLENE GLYCOL 3350, 200MM PROLINE, 100MM HEPES/NAOH, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953691 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953691 Å / Relative weight: 1 |
Reflection | Resolution: 4.4→50 Å / Num. obs: 17344 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 182.16 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 2.77 |
Reflection shell | Resolution: 4.4→4.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 1064 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZXB Resolution: 4.4→42.49 Å / Cor.coef. Fo:Fc: 0.9144 / Cor.coef. Fo:Fc free: 0.8767 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.152 Details: The apparent discrepancy in calculated Rwork/Rfree from reported by depositor is use of expectation values in calculation by BUSTER
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Displacement parameters | Biso mean: 247.62 Å2
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Refine analyze | Luzzati coordinate error obs: 1.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 4.4→42.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.4→4.67 Å / Total num. of bins used: 9
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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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