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- PDB-4y14: Structure of protein tyrosine phosphatase 1B complexed with inhib... -

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Basic information

Entry
Database: PDB / ID: 4y14
TitleStructure of protein tyrosine phosphatase 1B complexed with inhibitor (PTP1B:CPT157633)
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE/INHIBITOR / Tyrosine inhibitor complex / HYDROLASE / PROTEIN BINDING / HYDROLASE-INHIBITOR complex
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 superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-C0A / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.898 Å
AuthorsChoy, M.S. / Connors, C. / Page, R. / Peti, W.
CitationJournal: J.Clin.Invest. / Year: 2015
Title: PTP1B inhibition suggests a therapeutic strategy for Rett syndrome.
Authors: Krishnan, N. / Krishnan, K. / Connors, C.R. / Choy, M.S. / Page, R. / Peti, W. / Van Aelst, L. / Shea, S.D. / Tonks, N.K.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,16013
Polymers71,5932
Non-polymers1,56611
Water9,710539
1
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7058
Polymers35,7971
Non-polymers9087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4555
Polymers35,7971
Non-polymers6584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.167, 71.748, 88.010
Angle α, β, γ (deg.)90.000, 94.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPchain AAA2 - 2987 - 303
2PROPROchain BBB2 - 3017 - 306

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35796.746 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 550 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-C0A / 3-bromo-4-[difluoro(phosphono)methyl]-N-methyl-Nalpha-(methylsulfonyl)-L-phenylalaninamide


Mass: 465.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16BrF2N2O6PS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Tris, pH 7.4, 20% PEG8000, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46494 / % possible obs: 90.7 % / Redundancy: 7 % / Biso Wilson estimate: 20.95 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.035 / Net I/av σ(I): 28.67 / Net I/σ(I): 10.1 / Num. measured all: 326178
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.934.40.30712880.52349.4
1.93-1.974.80.27114480.52657.8
1.97-2.015.10.24216480.54764.2
2.01-2.055.40.21618920.55874.9
2.05-2.095.80.20222380.63387.7
2.09-2.146.70.18624610.64196.9
2.14-2.197.40.1624830.66997.3
2.19-2.257.40.14424880.73197.3
2.25-2.327.40.14625130.71697.6
2.32-2.397.50.12925030.72498
2.39-2.487.50.11325150.77798.3
2.48-2.587.50.10925010.78798.3
2.58-2.77.50.09525060.86198.6
2.7-2.847.50.08525440.9498.8
2.84-3.027.50.07425291.06299.2
3.02-3.257.50.06125751.21399.2
3.25-3.587.50.05125391.45699.6
3.58-4.097.50.04825781.82599.7
4.09-5.167.50.04426091.905100
5.16-507.30.04826362.07899.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å43.35 Å
Translation1.9 Å43.35 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data reduction
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
PHENIXmodel building
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C88

1c88


Resolution: 1.898→43.347 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 2266 4.88 %
Rwork0.1661 44176 -
obs0.1681 46442 90.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.86 Å2 / Biso mean: 25.0077 Å2 / Biso min: 7.21 Å2
Refinement stepCycle: final / Resolution: 1.898→43.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 85 539 5375
Biso mean--28.48 32.41 -
Num. residues----589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044934
X-RAY DIFFRACTIONf_angle_d0.8896668
X-RAY DIFFRACTIONf_chiral_restr0.036708
X-RAY DIFFRACTIONf_plane_restr0.005849
X-RAY DIFFRACTIONf_dihedral_angle_d13.1741836
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2796X-RAY DIFFRACTION1.54TORSIONAL
12B2796X-RAY DIFFRACTION1.54TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8983-1.93960.2434830.19521519160250
1.9396-1.98470.25441080.17961804191260
1.9847-2.03440.23961050.17562114221970
2.0344-2.08940.23011570.17452588274586
2.0894-2.15080.24161100.17412996310697
2.1508-2.22030.21331510.16552933308498
2.2203-2.29960.22661490.17182986313598
2.2996-2.39170.21661330.17752993312698
2.3917-2.50050.2131610.17632967312898
2.5005-2.63230.25231320.18563017314998
2.6323-2.79720.2331420.18663009315199
2.7972-3.01310.23031490.18923021317099
3.0131-3.31630.20571650.17853031319699
3.3163-3.79590.17791670.149530403207100
3.7959-4.78150.18221630.13553058322199
4.7815-43.3580.1791910.157331003291100

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