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- PDB-8dwn: Crystal structure of bis-phosphorylated insulin receptor kinase domain -

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Basic information

Entry
Database: PDB / ID: 8dwn
TitleCrystal structure of bis-phosphorylated insulin receptor kinase domain
ComponentsInsulin receptor subunit beta
KeywordsTRANSFERASE / insulin receptor / tyrosine kinase / phosphorylation
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 / exocrine pancreas development / positive regulation of protein-containing complex disassembly / 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 / exocrine pancreas development / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cargo receptor activity / insulin binding / neuronal cell body membrane / 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 / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / transport across blood-brain barrier / heart morphogenesis / activation of protein kinase B activity / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of glycolytic process / learning / positive regulation of D-glucose import / 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 / 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 / positive regulation of nitric oxide biosynthetic process / late endosome / insulin receptor signaling pathway / glucose homeostasis / amyloid-beta binding / positive regulation of protein phosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein autophosphorylation / protein tyrosine kinase activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / endosome membrane / positive regulation of cell migration / protein phosphorylation / G protein-coupled receptor signaling pathway / protein domain specific binding / symbiont entry into host cell / axon / external side of plasma membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein-containing complex binding / GTP binding / positive regulation of DNA-templated transcription / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
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. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...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. / 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 / 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 / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHubbard, S.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK052916 United States
CitationJournal: To Be Published
Title: Crystal structure of bis-phosphorylated insulin receptor kinase domain
Authors: Hubbard, S.R.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin receptor subunit beta


Theoretical massNumber of molelcules
Total (without water)34,9531
Polymers34,9531
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.943, 70.189, 88.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Insulin receptor subunit beta


Mass: 34952.762 Da / Num. of mol.: 1 / Mutation: C981S, Y984F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06213
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 6000, 0.2 M malate-imidazole

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 9, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→32.64 Å / Num. obs: 18050 / % possible obs: 88.93 % / Redundancy: 2.3 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0483 / Rpim(I) all: 0.0356 / Net I/σ(I): 14.78
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 6.83 / Num. unique obs: 1788 / CC1/2: 0.947 / CC star: 0.986 / Rpim(I) all: 0.119 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IRK

1irk


Resolution: 2.15→32.64 Å / SU ML: 0.2362 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 1805 10 %
Rwork0.1896 16245 -
obs0.1954 18050 88.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.93 Å2
Refinement stepCycle: LAST / Resolution: 2.15→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 219 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012296
X-RAY DIFFRACTIONf_angle_d0.96893107
X-RAY DIFFRACTIONf_chiral_restr0.0579339
X-RAY DIFFRACTIONf_plane_restr0.0118402
X-RAY DIFFRACTIONf_dihedral_angle_d8.2635309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.27861380.19541235X-RAY DIFFRACTION89.86
2.21-2.270.27891410.19541267X-RAY DIFFRACTION91.91
2.27-2.350.30221400.2131278X-RAY DIFFRACTION92.44
2.35-2.430.27061410.20241258X-RAY DIFFRACTION91.62
2.43-2.530.27891420.19731278X-RAY DIFFRACTION91.38
2.53-2.640.28411390.20421253X-RAY DIFFRACTION91.16
2.64-2.780.27561390.21341252X-RAY DIFFRACTION89.92
2.78-2.960.28581390.19841253X-RAY DIFFRACTION89.69
2.96-3.180.25711380.20891241X-RAY DIFFRACTION88.28
3.18-3.50.23381380.19381238X-RAY DIFFRACTION88.32
3.51-4.010.2161360.16931228X-RAY DIFFRACTION86.71
4.01-5.050.20861380.16041246X-RAY DIFFRACTION85.96
5.05-32.640.22481360.18721218X-RAY DIFFRACTION80.55

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