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- PDB-8eya: Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain w... -

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Basic information

Entry
Database: PDB / ID: 8eya
TitleCrystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with a JAK2 activation loop phosphopeptide
Components(Tyrosine-protein ...) x 2
KeywordsSIGNALING PROTEIN / PTP1B / JAK/STAT / IRK
Function / homology
Function and homology information


interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex ...interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / Signaling by Erythropoietin / collagen-activated signaling pathway / interleukin-12 receptor binding / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / response to interleukin-12 / Erythropoietin activates Phospholipase C gamma (PLCG) / positive regulation of leukocyte proliferation / post-embryonic hemopoiesis / interleukin-12 receptor complex / activation of Janus kinase activity / tyrosine phosphorylation of STAT protein / interleukin-23 receptor complex / positive regulation of MHC class II biosynthetic process / positive regulation of platelet aggregation / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of platelet activation / acetylcholine receptor binding / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / Signaling by Leptin / regulation of nitric oxide biosynthetic process / positive regulation of signaling receptor activity / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / positive regulation of epithelial cell apoptotic process / response to hydroperoxide / positive regulation of natural killer cell proliferation / positive regulation of cell-substrate adhesion / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / axon regeneration / growth hormone receptor signaling pathway / peptide hormone receptor binding / negative regulation of cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / regulation of hepatocyte growth factor receptor signaling pathway / extrinsic component of plasma membrane / PTK6 Down-Regulation / IFNG signaling activates MAPKs / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of cell-cell adhesion / Interleukin-6 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / 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 / Prolactin receptor signaling / IRE1-mediated unfolded protein response / MAPK3 (ERK1) activation / response to amine / positive regulation of interleukin-17 production / negative regulation of DNA binding / positive regulation of nitric-oxide synthase biosynthetic process / 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 / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / mesoderm development / regulation of type I interferon-mediated signaling pathway / positive regulation of SMAD protein signal transduction / platelet-derived growth factor receptor signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / response to tumor necrosis factor / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / 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 ...Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / 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 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 / SH2 domain / 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. / 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
Tyrosine-protein kinase JAK2 / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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 26, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
B: Tyrosine-protein phosphatase non-receptor type 1
D: Tyrosine-protein kinase JAK2 activation loop phosphopeptide
E: Tyrosine-protein kinase JAK2 activation loop phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,62314
Polymers74,1664
Non-polymers45710
Water3,153175
1
A: Tyrosine-protein phosphatase non-receptor type 1
D: Tyrosine-protein kinase JAK2 activation loop phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4209
Polymers37,0832
Non-polymers3377
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-47 kcal/mol
Surface area13830 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 1
E: Tyrosine-protein kinase JAK2 activation loop phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2045
Polymers37,0832
Non-polymers1213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-33 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.833, 88.833, 197.456
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 24 or resid 26...
21(chain B and (resid 2 through 4 or (resid 5...
12chain D
22(chain E and (resid 1005 through 1009 or (resid 1010...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 24 or resid 26...A2 - 24
121(chain A and (resid 2 through 24 or resid 26...A26 - 31
131(chain A and (resid 2 through 24 or resid 26...A33 - 46
141(chain A and (resid 2 through 24 or resid 26...A47
151(chain A and (resid 2 through 24 or resid 26...A2 - 302
161(chain A and (resid 2 through 24 or resid 26...A2 - 302
171(chain A and (resid 2 through 24 or resid 26...A2 - 302
181(chain A and (resid 2 through 24 or resid 26...A2 - 302
191(chain A and (resid 2 through 24 or resid 26...A2 - 302
1101(chain A and (resid 2 through 24 or resid 26...A2 - 302
211(chain B and (resid 2 through 4 or (resid 5...B2 - 4
221(chain B and (resid 2 through 4 or (resid 5...B5
231(chain B and (resid 2 through 4 or (resid 5...B2 - 299
241(chain B and (resid 2 through 4 or (resid 5...B2 - 299
251(chain B and (resid 2 through 4 or (resid 5...B2 - 299
261(chain B and (resid 2 through 4 or (resid 5...B2 - 299
112chain DD1005 - 1010
212(chain E and (resid 1005 through 1009 or (resid 1010...E0

NCS ensembles :
ID
1
2

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Components

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Tyrosine-protein ... , 2 types, 4 molecules ABDE

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


Mass: 34997.910 Da / Num. of mol.: 2 / Mutation: D181A/Q262A/C215A
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 JAK2 activation loop phosphopeptide / Janus kinase 2 / JAK-2


Mass: 2085.119 Da / Num. of mol.: 2 / Fragment: residues 1000-1015 of JAK2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O60674, non-specific protein-tyrosine kinase

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Non-polymers , 5 types, 185 molecules

#3: 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 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop
Details: 25% w/v PEG 3350, 0.2 M NaCl, 0.1 M Tris Cl (pH 8.5)

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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: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.01→44.416 Å / Num. obs: 53433 / % possible obs: 99.67 % / Redundancy: 5 % / CC1/2: 0.99 / Net I/σ(I): 16.67
Reflection shellResolution: 2.01→2.17 Å / Num. unique obs: 5267 / CC1/2: 0.85

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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: 1SUG

1sug


Resolution: 2.099→44.416 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1993 3.73 %
Rwork0.2206 51440 -
obs0.2221 53433 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.99 Å2 / Biso mean: 50.3722 Å2 / Biso min: 26.83 Å2
Refinement stepCycle: final / Resolution: 2.099→44.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 29 175 5063
Biso mean--60.75 50.41 -
Num. residues----610
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2769X-RAY DIFFRACTION8.529TORSIONAL
12B2769X-RAY DIFFRACTION8.529TORSIONAL
21D26X-RAY DIFFRACTION8.529TORSIONAL
22E26X-RAY DIFFRACTION8.529TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0994-2.15190.38691370.3357360899
2.1519-2.210.38041400.31383633100
2.21-2.27510.35291400.3063646100
2.2751-2.34850.33951430.30543599100
2.3485-2.43240.33851400.28783642100
2.4324-2.52980.35181410.27113673100
2.5298-2.64490.30051410.27093626100
2.6449-2.78440.2671440.26053669100
2.7844-2.95880.26281450.2563681100
2.9588-3.18720.25941380.24373651100
3.1872-3.50780.27421420.22863693100
3.5078-4.01510.25781400.1923369499
4.0151-5.05750.19781460.1715373199
5.0575-44.4160.22671560.1828389499

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