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- PDB-1qqg: CRYSTAL STRUCTURE OF THE PH-PTB TARGETING REGION OF IRS-1 -

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Basic information

Entry
Database: PDB / ID: 1qqg
TitleCRYSTAL STRUCTURE OF THE PH-PTB TARGETING REGION OF IRS-1
ComponentsINSULIN RECEPTOR SUBSTRATE 1IRS1
KeywordsSIGNAL TRANSDUCTION / BETA-SANDWHICH
Function / homology
Function and homology information


IRS-related events triggered by IGF1R / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin receptor complex / positive regulation of glucose metabolic process / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by Leptin / PI3K/AKT activation / cellular response to fatty acid ...IRS-related events triggered by IGF1R / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin receptor complex / positive regulation of glucose metabolic process / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by Leptin / PI3K/AKT activation / cellular response to fatty acid / Signaling by ALK / IRS activation / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / PI3K Cascade / negative regulation of insulin secretion / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / Growth hormone receptor signaling / positive regulation of insulin receptor signaling pathway / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / Interleukin-7 signaling / SH2 domain binding / phosphotyrosine residue binding / protein kinase C binding / insulin-like growth factor receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / positive regulation of glucose import / response to insulin / insulin receptor binding / cytokine-mediated signaling pathway / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / signaling receptor complex adaptor activity / glucose homeostasis / PIP3 activates AKT signaling / insulin receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / signal transduction / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Insulin receptor substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDhe-Paganon, S. / Shoelson, S.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of the pleckstrin homology-phosphotyrosine binding (PH-PTB) targeting region of insulin receptor substrate 1.
Authors: Dhe-Paganon, S. / Ottinger, E.A. / Nolte, R.T. / Eck, M.J. / Shoelson, S.E.
History
DepositionJun 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 SUBSTRATE 1


Theoretical massNumber of molelcules
Total (without water)58,3122
Polymers58,3122
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.439, 120.439, 79.598
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein INSULIN RECEPTOR SUBSTRATE 1 / IRS1 / IRS-1


Mass: 29156.021 Da / Num. of mol.: 2 / Fragment: PH-PTB (N-TERMINAL DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P35568
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.7M SODIUM PHOSPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMTris1drop
3200 mM1dropNaCl
410 mMdithiothreitol1drop
51.7 Msodium phosphate1reservoir
610 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 93545 / Num. obs: 91581 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.11 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.94
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.41 / % possible all: 98.3
Reflection
*PLUS
Num. obs: 29443 / Num. measured all: 91581

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.843refinement
XDSdata reduction
AUTOMARdata reduction
RefinementResolution: 2.3→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.247 1240 RANDOM
Rwork0.191 --
obs0.191 26412 -
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 168 3526
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.38

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