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- PDB-7mn9: PTP1B 1-284 F225Y-R199N -

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Basic information

Entry
Database: PDB / ID: 7mn9
TitlePTP1B 1-284 F225Y-R199N
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PROTEIN TYROSINE PHOSPHATASE
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / 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 / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / 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 / 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 / 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 / insulin receptor binding / cellular response to nerve growth factor stimulus / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / mitochondrial matrix / cadherin binding / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsTorgeson, K.R. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
American Diabetes Association1-14-ACN-31 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098482 United States
CitationJournal: Sci Adv / Year: 2022
Title: Conserved conformational dynamics determine enzyme activity.
Authors: Torgeson, K.R. / Clarkson, M.W. / Granata, D. / Lindorff-Larsen, K. / Page, R. / Peti, W.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9767
Polymers33,5061
Non-polymers4696
Water6,431357
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)88.464, 88.464, 72.429
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 33506.309 Da / Num. of mol.: 1 / Mutation: F225Y, R199N
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, .1 M Tris pH 7.6, 18.5% PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.24→38.31 Å / Num. obs: 92834 / % possible obs: 99.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.9
Reflection shellResolution: 1.24→1.26 Å / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4211 / CC1/2: 0.999 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k9v

5k9v


Resolution: 1.24→38.31 Å / SU ML: 0.1114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1801 4841 5.25 %
Rwork0.1622 87304 -
obs0.1631 92145 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.57 Å2
Refinement stepCycle: LAST / Resolution: 1.24→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 28 357 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01632424
X-RAY DIFFRACTIONf_angle_d1.49383292
X-RAY DIFFRACTIONf_chiral_restr0.1106353
X-RAY DIFFRACTIONf_plane_restr0.0097428
X-RAY DIFFRACTIONf_dihedral_angle_d14.7392924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.27831690.25712907X-RAY DIFFRACTION99.71
1.26-1.270.23461470.24742859X-RAY DIFFRACTION99.77
1.27-1.290.20011780.23092889X-RAY DIFFRACTION99.97
1.29-1.30.22871330.21662911X-RAY DIFFRACTION99.97
1.3-1.320.23911650.21722854X-RAY DIFFRACTION99.8
1.32-1.340.24831400.2062906X-RAY DIFFRACTION99.84
1.34-1.360.18691360.19962920X-RAY DIFFRACTION99.97
1.36-1.380.20671580.19042907X-RAY DIFFRACTION99.93
1.38-1.40.18741530.1892866X-RAY DIFFRACTION100
1.4-1.420.18271370.18422917X-RAY DIFFRACTION100
1.42-1.450.20071500.1812936X-RAY DIFFRACTION100
1.45-1.470.1691550.16712892X-RAY DIFFRACTION100
1.47-1.50.17381760.1652876X-RAY DIFFRACTION100
1.5-1.530.19221610.16422876X-RAY DIFFRACTION99.38
1.53-1.560.16291400.15212901X-RAY DIFFRACTION99.18
1.56-1.60.17051610.15392898X-RAY DIFFRACTION100
1.6-1.640.19581450.15162906X-RAY DIFFRACTION100
1.64-1.690.16071670.15032889X-RAY DIFFRACTION100
1.69-1.740.17841720.15342910X-RAY DIFFRACTION100
1.74-1.790.19951710.14872891X-RAY DIFFRACTION100
1.79-1.860.16381640.15522911X-RAY DIFFRACTION100
1.86-1.930.18161790.15132888X-RAY DIFFRACTION99.26
1.93-2.020.14631800.15262901X-RAY DIFFRACTION100
2.02-2.120.1691820.15122905X-RAY DIFFRACTION100
2.12-2.260.18181700.14382923X-RAY DIFFRACTION100
2.26-2.430.17531800.16152901X-RAY DIFFRACTION99.87
2.43-2.680.19061710.16482942X-RAY DIFFRACTION99.74
2.68-3.060.18151670.16332939X-RAY DIFFRACTION99.62
3.06-3.860.17251490.14963012X-RAY DIFFRACTION100
3.86-38.310.17751850.16273071X-RAY DIFFRACTION99.54
Refinement TLS params.Method: refined / Origin x: -27.2418823232 Å / Origin y: 18.0240126638 Å / Origin z: 4.23700997965 Å
111213212223313233
T0.126462409925 Å2-0.0286866638829 Å2-0.0167471741161 Å2-0.0863010490562 Å20.0228857912072 Å2--0.091932484421 Å2
L0.665734341717 °20.299131026159 °20.15396872105 °2-1.05350390728 °2-0.067710124706 °2--0.420358372795 °2
S0.0923222057228 Å °-0.0503123159104 Å °-0.076805062682 Å °0.0961074068081 Å °-0.097174089129 Å °-0.1173451739 Å °0.0560353676966 Å °0.0177299025413 Å °-0.0015564057244 Å °
Refinement TLS groupSelection details: all

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