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Yorodumi- PDB-3w13: Insulin receptor ectodomain construct comprising domains L1-CR in... -
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-Basic information
Entry | Database: PDB / ID: 3w13 | |||||||||
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Title | Insulin receptor ectodomain construct comprising domains L1-CR in complex with high-affinity insulin analogue [D-PRO-B26]-DTI-NH2, alphact peptide(693-719) and FAB 83-7 | |||||||||
Components |
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Keywords | HORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM / CELL SURFACE RECEPTOR/IMMUNE SYSTEM / INSULIN RECEPTOR / IR ECTODOMAIN / CT PEPTIDE / INSULIN ANALOGUE / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM COMPLEX | |||||||||
Function / homology | Function and homology information regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly ...regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / adrenal gland development / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / Insulin processing / neuronal cell body membrane / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / positive regulation of receptor internalization / alpha-beta T cell activation / regulation of embryonic development / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / transport across blood-brain barrier / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / phosphatidylinositol 3-kinase binding / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / heart morphogenesis / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of MAP kinase activity / positive regulation of nitric-oxide synthase activity / learning / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / caveola / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / receptor protein-tyrosine kinase / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / peptidyl-tyrosine phosphorylation / regulation of synaptic plasticity / vasodilation / hormone activity / cellular response to insulin stimulus / receptor internalization / memory / cognition / cellular response to growth factor stimulus / positive regulation of neuron projection development Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.303 Å | |||||||||
Authors | Lawrence, M.C. / Smith, B.J. / Brzozowski, A.M. | |||||||||
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.-W. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / ...Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K.-W. / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w13.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w13.ent.gz | 209.1 KB | Display | PDB format |
PDBx/mmJSON format | 3w13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w13_validation.pdf.gz | 969 KB | Display | wwPDB validaton report |
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Full document | 3w13_full_validation.pdf.gz | 983 KB | Display | |
Data in XML | 3w13_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 3w13_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/3w13 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/3w13 | HTTPS FTP |
-Related structure data
Related structure data | 3w11C 3w12C 5kqvC 2wrwS 3loh 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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Unit cell |
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-Components
-Insulin receptor ... , 2 types, 2 molecules EF
#1: Protein | Mass: 35503.934 Da / Num. of mol.: 1 / Fragment: UNP residues 28-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell (production host): CHO CELL / Cell line (production host): LEC8 MUTANT / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P06213, receptor protein-tyrosine kinase |
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#6: Protein/peptide | Mass: 2788.073 Da / Num. of mol.: 1 / Fragment: UNP residues 724-746 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) HOMO SAPIENS (human) References: UniProt: P06213, receptor protein-tyrosine kinase |
-Protein/peptide , 2 types, 2 molecules AB
#4: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: semi-synthetic modification of porcine insulin derived from porcine pancreas Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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#5: Protein/peptide | Mass: 2938.408 Da / Num. of mol.: 1 / Fragment: UNP residues 25-50 / Source method: obtained synthetically Details: semi-synthetic modification of porcine insulin derived from porcine pancreas Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
-Antibody , 2 types, 2 molecules CD
#2: Antibody | Mass: 12712.239 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse) |
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#3: Antibody | Mass: 12684.292 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse) |
-Sugars , 3 types, 4 molecules
#7: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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 |
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#8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 |
-Details
Sequence details | HIS E 144 IS NATURAL VARIANT RS1051692. THE SEQUENCE OF CHIAN F IS ISOFORM SHORT OF INSULIN ...HIS E 144 IS NATURAL VARIANT RS1051692. THE SEQUENCE OF CHIAN F IS ISOFORM SHORT OF INSULIN RECEPTOR, P06213-2. B26 TYR MUTATED TO D-PRO; B27-B30 ARE DELETED; B26 C-TERMINUS IS FINISHED WITH CONH2 (CARBOXYAMI |
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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: 5.968 Å3/Da / Density % sol: 79.39 % / Mosaicity: 0.1 ° |
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Crystal grow | pH: 8 Details: 0.9-1.1M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE-HCL, 0.02% SOIDUM AZIDE, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 4.303→169.228 Å / Num. all: 11033 / Num. obs: 11033 / % possible obs: 98.5 % / Redundancy: 4.4 % / Rsym value: 0.101 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 4.303→4.54 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.4 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LOH,2WRW Resolution: 4.303→29.48 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.856 / SU B: 160.517 / SU ML: 0.868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.974 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 226.59 Å2
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Refinement step | Cycle: LAST / Resolution: 4.303→29.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.303→4.41 Å / Total num. of bins used: 20
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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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