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- PDB-2b4s: Crystal structure of a complex between PTP1B and the insulin rece... -

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Basic information

Entry
Database: PDB / ID: 2b4s
TitleCrystal structure of a complex between PTP1B and the insulin receptor tyrosine kinase
Components
  • Insulin receptor
  • Tyrosine-protein phosphatase, non-receptor type 1
KeywordsHydrolase/transferase / phosphorylation / tyrosine protein kinase / Hydrolase-transferase 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 / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / exocrine pancreas development / dendritic spine maintenance ...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 / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / exocrine pancreas development / dendritic spine maintenance / cargo receptor activity / insulin binding / adrenal gland development / PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / PTB domain binding / positive regulation of receptor catabolic process / neuronal cell body membrane / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / IRE1-mediated unfolded protein response / Signaling by Insulin receptor / regulation of intracellular protein transport / IRS activation / positive regulation of protein tyrosine kinase activity / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / cytoplasmic side of endoplasmic reticulum membrane / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / positive regulation of respiratory burst / amyloid-beta clearance / positive regulation of JUN kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / negative regulation of MAP kinase activity / regulation of endocytosis / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / peptidyl-tyrosine dephosphorylation / regulation of embryonic development / Regulation of IFNA/IFNB signaling / positive regulation of receptor internalization / cellular response to angiotensin / regulation of proteolysis / insulin receptor substrate binding / protein kinase activator activity / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / growth hormone receptor signaling pathway via JAK-STAT / epidermis development / cellular response to unfolded protein / regulation of signal transduction / positive regulation of glycogen biosynthetic process / Signal attenuation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNG signaling / negative regulation of signal transduction / heart morphogenesis / Growth hormone receptor signaling / positive regulation of heart rate / transport across blood-brain barrier / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cardiac muscle cell apoptotic process / endoplasmic reticulum unfolded protein response / protein dephosphorylation / phosphatidylinositol 3-kinase binding / MECP2 regulates neuronal receptors and channels / insulin receptor activity / Insulin receptor recycling / cellular response to fibroblast growth factor stimulus / cellular response to platelet-derived growth factor stimulus / insulin-like growth factor receptor binding / ephrin receptor binding / Integrin signaling / neuron projection maintenance / dendrite membrane / protein-tyrosine-phosphatase / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / receptor-mediated endocytosis / protein phosphatase 2A binding / positive regulation of glycolytic process / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / positive regulation of D-glucose import / response to nutrient levels / learning / insulin receptor binding / cellular response to nerve growth factor stimulus / Negative regulation of MET activity / receptor protein-tyrosine kinase
Similarity search - Function
Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Protein tyrosine phosphatase superfamily / Receptor L-domain / Furin-like cysteine-rich domain ...Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Protein tyrosine phosphatase superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Protein-Tyrosine Phosphatase; Chain A / Furin-like repeat / Furin-like repeats / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Growth factor receptor cysteine-rich domain superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Insulin receptor / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, S. / Depetris, R.S. / Barford, D. / Chernoff, J. / Hubbard, S.R.
CitationJournal: Structure / Year: 2005
Title: Crystal Structure of a Complex between Protein Tyrosine Phosphatase 1B and the Insulin Receptor Tyrosine Kinase.
Authors: Li, S. / Depetris, R.S. / Barford, D. / Chernoff, J. / Hubbard, S.R.
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase, non-receptor type 1
B: Insulin receptor
C: Tyrosine-protein phosphatase, non-receptor type 1
D: Insulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,40514
Polymers139,4444
Non-polymers96110
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.472, 88.165, 178.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein phosphatase, non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 34688.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Protein Insulin receptor / IR / CD220 antigen


Mass: 35033.660 Da / Num. of mol.: 2 / Fragment: Protein kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P06213, EC: 2.7.1.112
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris-HCl, 1.9 M ammonium sulfate, 2% PEG 400, pH 7.5, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: Apr 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 61660 / Num. obs: 60480 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.104
Reflection shellResolution: 2.3→2.37 Å / Rmerge(I) obs: 0.272 / % possible all: 94.2

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IR3, 1G1H

1ir3

1g1h


Resolution: 2.3→29.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 175542.24 / Data cutoff high rms absF: 175542.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2946 5.1 %RANDOM
Rwork0.208 ---
obs0.208 58237 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.272 Å2 / ksol: 0.357338 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2--0.28 Å20 Å2
3----4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9214 0 50 377 9641
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_mcangle_it1.432
X-RAY DIFFRACTIONc_scbond_it1.312
X-RAY DIFFRACTIONc_scangle_it2.052.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 497 5.7 %
Rwork0.249 8206 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4paramcsdx.misc
X-RAY DIFFRACTION5dna-rna.param

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