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- PDB-8exm: Crystal structure of PTP1B D181A/Q262A phosphatase domain with a ... -

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Basic information

Entry
Database: PDB / ID: 8exm
TitleCrystal structure of PTP1B D181A/Q262A phosphatase domain with a JAK3 activation loop phosphopeptide
Components
  • Tyrosine-protein kinase JAK3 activation loop peptide
  • Tyrosine-protein phosphatase non-receptor type 1
KeywordsSIGNALING PROTEIN / PTP1B / JAK/STAT / IRK
Function / homology
Function and homology information


negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling ...negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of T cell apoptotic process / negative regulation of interleukin-12 production / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / extrinsic component of plasma membrane / regulation of hepatocyte growth factor receptor signaling pathway / Signaling by ALK / PTK6 Down-Regulation / Interleukin-20 family signaling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / negative regulation of interleukin-10 production / insulin receptor recycling / enzyme-linked receptor protein signaling pathway / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / T cell homeostasis / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / cell surface receptor signaling pathway via JAK-STAT / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / extrinsic component of cytoplasmic side of plasma membrane / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / Interleukin-7 signaling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / B cell differentiation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / endosome lumen / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / insulin receptor signaling pathway / actin cytoskeleton organization / RAF/MAP kinase cascade / regulation of apoptotic process / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / cell differentiation / early endosome / cytoskeleton / endosome / intracellular signal transduction / mitochondrial matrix / cadherin binding / protein phosphorylation / innate immune response / protein kinase binding
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak3 / 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 / 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 domain ...Tyrosine-protein kinase, non-receptor Jak3 / 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 / 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 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 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 JAK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 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 JAK3 activation loop peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8584
Polymers36,6412
Non-polymers2172
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.590, 88.590, 132.165
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: 34733.648 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 JAK3 activation loop peptide / Janus kinase 3 / JAK-3 / Leukocyte janus kinase / L-JAK


Mass: 1907.171 Da / Num. of mol.: 1 / Fragment: residues 973-988 of JAK3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P52333, 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.: 1 / 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.: 86 / 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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop
Details: 12% Peg 4K, 0.15 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 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.349→39.62 Å / Num. obs: 22507 / % possible obs: 99.49 % / Redundancy: 11.4 % / CC1/2: 0.1 / Net I/σ(I): 27.61
Reflection shellResolution: 2.349→2.43 Å / Num. unique obs: 2118 / CC1/2: 0.91

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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: 2.349→39.619 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1996 8.87 %
Rwork0.206 20511 -
obs0.2096 22507 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.91 Å2 / Biso mean: 61.5873 Å2 / Biso min: 35.21 Å2
Refinement stepCycle: final / Resolution: 2.349→39.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 25 86 2504
Biso mean--72.76 58.01 -
Num. residues----302
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3495-2.40820.31521330.2683136694
2.4082-2.47330.26991380.2479141899
2.4733-2.54610.32291400.24721441100
2.5461-2.62820.31381390.25941441100
2.6282-2.72210.29271420.25471448100
2.7221-2.83110.33251420.26671456100
2.8311-2.95990.31461410.2651450100
2.9599-3.11590.31981420.26791463100
3.1159-3.3110.29831420.24211463100
3.311-3.56650.26521440.22431470100
3.5665-3.92520.22681430.20281466100
3.9252-4.49250.21381450.16721499100
4.4925-5.65740.19361460.16271517100
5.6574-39.6190.22151590.18521613100

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