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- PDB-8exj: Crystal structure of PTP1B D181A/Q262A phosphatase domain in comp... -

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Basic information

Entry
Database: PDB / ID: 8exj
TitleCrystal structure of PTP1B D181A/Q262A phosphatase domain in complex with a JAK1 activation loop phosphopeptide
Components
  • Tyrosine-protein kinase JAK1 activation loop peptide
  • Tyrosine-protein phosphatase non-receptor type 1
KeywordsSIGNALING PROTEIN / PTP1B / JAK/STAT / IRK
Function / homology
Function and homology information


type III interferon-mediated signaling pathway / protein localization to cell-cell junction / interleukin-10-mediated signaling pathway / CCR5 chemokine receptor binding / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway ...type III interferon-mediated signaling pathway / protein localization to cell-cell junction / interleukin-10-mediated signaling pathway / CCR5 chemokine receptor binding / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-12 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / Interleukin-35 Signalling / growth hormone receptor binding / Interleukin-15 signaling / Interleukin-2 signaling / extrinsic component of cytoplasmic side of plasma membrane / Other interleukin signaling / Interleukin-20 family signaling / Interleukin-6 signaling / PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / type I interferon-mediated signaling pathway / positive regulation of receptor catabolic process / IFNG signaling activates MAPKs / insulin receptor recycling / MAPK3 (ERK1) activation / negative regulation of vascular endothelial growth factor receptor signaling pathway / interleukin-6-mediated signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / positive regulation of sprouting angiogenesis / MAPK1 (ERK2) activation / Interleukin-10 signaling / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of vascular associated smooth muscle cell migration / 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 / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / regulation of proteolysis / positive regulation of JUN kinase activity / cellular response to fibroblast growth factor stimulus / growth hormone receptor signaling pathway via JAK-STAT / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / cell surface receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / type II interferon-mediated signaling pathway / Interleukin receptor SHC signaling / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Signaling by CSF3 (G-CSF) / endoplasmic reticulum unfolded protein response / positive regulation of cardiac muscle cell apoptotic process / MECP2 regulates neuronal receptors and channels / protein dephosphorylation / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / Integrin signaling / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / Interleukin-7 signaling / negative regulation of insulin receptor signaling pathway / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / insulin receptor binding / cellular response to nerve growth factor stimulus / response to nutrient levels / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak1 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / : / SH2 domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain ...Tyrosine-protein kinase, non-receptor Jak1 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / : / SH2 domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / Protein-tyrosine phosphatase, non-receptor type-1/2 / : / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 1 / Tyrosine-protein kinase JAK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsMorris, R. / Kershaw, N.J. / Babon, J.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Commun Biol / Year: 2023
Title: Structure guided studies of the interaction between PTP1B and JAK.
Authors: Morris, R. / Keating, N. / Tan, C. / Chen, H. / Laktyushin, A. / Saiyed, T. / Liau, N.P.D. / Nicola, N.A. / Tiganis, T. / Kershaw, N.J. / Babon, J.J.
History
DepositionOct 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
D: Tyrosine-protein kinase JAK1 activation loop peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9925
Polymers36,6532
Non-polymers3393
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.578, 88.578, 132.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 34732.664 Da / Num. of mol.: 1 / Mutation: D181A/Q262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Protein/peptide Tyrosine-protein kinase JAK1 activation loop peptide / Janus kinase 1 / JAK-1


Mass: 1920.033 Da / Num. of mol.: 1 / Fragment: residues 1027-1042 of JAK1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P23458, non-specific protein-tyrosine kinase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop
Details: 12% Peg 4K, 0.1 M Calcium acetate, 0.05 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.301→45.503 Å / Num. obs: 24067 / % possible obs: 97.33 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1511 / Net I/σ(I): 9.56
Reflection shellResolution: 2.301→2.383 Å / Rmerge(I) obs: 4.248 / Num. unique obs: 2349 / CC1/2: 0.11

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PTY

1pty


Resolution: 2.301→45.503 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1942 8.28 %
Rwork0.2069 21509 -
obs0.2094 23451 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.84 Å2 / Biso mean: 69.3133 Å2 / Biso min: 43.39 Å2
Refinement stepCycle: final / Resolution: 2.301→45.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 45 52 2523
Biso mean--92.98 62.21 -
Num. residues----305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.301-2.35840.4645950.4235106568
2.3584-2.42210.40291290.3789144294
2.4221-2.49340.36621400.34511544100
2.4934-2.57390.35381410.32031549100
2.5739-2.66590.37551400.30821557100
2.6659-2.77260.33391410.29411561100
2.7726-2.89880.35791410.30321546100
2.8988-3.05150.30811390.26551568100
3.0515-3.24270.29581420.24181559100
3.2427-3.4930.28661430.22581579100
3.493-3.84430.21611430.1921582100
3.8443-4.40020.20781450.16311597100
4.4002-5.54220.17291460.1541635100
5.5422-45.5030.18211570.17081725100

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