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- PDB-5u1m: Structure of the IRS-1 PTB Domain Bound to the Juxtamembrane Regi... -

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Basic information

Entry
Database: PDB / ID: 5u1m
TitleStructure of the IRS-1 PTB Domain Bound to the Juxtamembrane Region of the Insulin Receptor
Components
  • Insulin receptor
  • Insulin receptor substrate 1
KeywordsPROTEIN BINDING / PTB domain / Insulin Receptor Substrate-1 / Phosphopeptide / Insulin Receptor
Function / homology
Function and homology information


IRS-related events triggered by IGF1R / regulation of female gonad development / positive regulation of meiotic cell cycle / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / positive regulation of glucose metabolic process ...IRS-related events triggered by IGF1R / regulation of female gonad development / positive regulation of meiotic cell cycle / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / positive regulation of glucose metabolic process / insulin-like growth factor I binding / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / exocrine pancreas development / positive regulation of protein-containing complex disassembly / Signaling by Leptin / Signaling by LTK / dendritic spine maintenance / PI3K/AKT activation / cargo receptor activity / insulin binding / cellular response to fatty acid / neuronal cell body membrane / Signaling by ALK / adrenal gland development / PTB domain binding / Signaling by Insulin receptor / IRS activation / positive regulation of respiratory burst / amyloid-beta clearance / regulation of embryonic development / positive regulation of receptor internalization / protein kinase activator activity / insulin receptor substrate binding / PI3K Cascade / SOS-mediated signalling / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / positive regulation of insulin receptor signaling pathway / transport across blood-brain barrier / negative regulation of insulin secretion / Growth hormone receptor signaling / heart morphogenesis / activation of protein kinase B activity / Insulin receptor recycling / insulin-like growth factor receptor binding / signaling adaptor activity / dendrite membrane / phosphotyrosine residue binding / neuron projection maintenance / positive regulation of MAP kinase activity / Interleukin-7 signaling / negative regulation of insulin receptor signaling pathway / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / SH2 domain binding / insulin-like growth factor receptor signaling pathway / positive regulation of glycolytic process / protein kinase C binding / learning / positive regulation of D-glucose import / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to insulin / insulin receptor binding / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / cytokine-mediated signaling pathway / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / caveola / receptor internalization / memory / cellular response to insulin stimulus / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / Signaling by ALK fusions and activated point mutants / late endosome / insulin receptor signaling pathway / glucose homeostasis / PIP3 activates AKT signaling / signaling receptor complex adaptor activity / amyloid-beta binding
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / PH domain / PH domain profile. / Pleckstrin homology domain. / Growth factor receptor cysteine-rich domain superfamily / Pleckstrin homology domain / Fibronectin type III domain / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Insulin receptor / Insulin receptor substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsEck, M.J. / Dhe-Paganon, S.
CitationJournal: Nat Commun / Year: 2017
Title: Domain-dependent effects of insulin and IGF-1 receptors on signalling and gene expression.
Authors: Cai, W. / Sakaguchi, M. / Kleinridders, A. / Gonzalez-Del Pino, G. / Dreyfuss, J.M. / O'Neill, B.T. / Ramirez, A.K. / Pan, H. / Winnay, J.N. / Boucher, J. / Eck, M.J. / Kahn, C.R.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin receptor substrate 1
B: Insulin receptor


Theoretical massNumber of molelcules
Total (without water)12,9242
Polymers12,9242
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.370, 68.370, 57.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Insulin receptor substrate 1 / IRS-1


Mass: 11832.777 Da / Num. of mol.: 1 / Fragment: PTB domain (UNP residues 161-265)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRS1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P35568
#2: Protein/peptide Insulin receptor / IR


Mass: 1091.066 Da / Num. of mol.: 1 / Fragment: juxtamembrane region (UNP residues 991-999)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P06213
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 12453 / % possible obs: 94.9 % / Redundancy: 6 % / Net I/σ(I): 15
Reflection shellHighest resolution: 1.8 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
MLPHAREphasing
RefinementResolution: 1.8→20 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs12453 94.9 %
Displacement parametersBiso max: 51.58 Å2 / Biso mean: 12.4704 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 120 1025

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