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- PDB-5kad: Protein Tyrosine Phosphatase 1B N193A mutant in complex with TCS4... -

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Basic information

Entry
Database: PDB / ID: 5kad
TitleProtein Tyrosine Phosphatase 1B N193A mutant in complex with TCS401, closed state
ComponentsTyrosine-protein phosphatase non-receptor type 1
Keywordshydrolase/hydrolase inhibitor / Protein tyrosine phosphatase / hydrolase-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 / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome ...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 / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / cytoplasmic side of endoplasmic reticulum membrane / 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 JUN kinase activity / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / positive regulation of systemic arterial blood pressure / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / cellular response to angiotensin / regulation of proteolysis / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / cellular response to unfolded protein / regulation of signal transduction / Regulation of IFNG signaling / negative regulation of signal transduction / Growth hormone receptor signaling / positive regulation of cardiac muscle cell apoptotic process / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein dephosphorylation / endoplasmic reticulum unfolded protein response / ephrin receptor binding / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / Integrin signaling / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / response to nutrient levels / Negative regulation of MET activity / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / cadherin binding / mitochondrial matrix / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-OTA / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
CitationJournal: Mol. Cell / Year: 2017
Title: Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.
Authors: Choy, M.S. / Li, Y. / Machado, L.E. / Kunze, M.B. / Connors, C.R. / Wei, X. / Lindorff-Larsen, K. / Page, R. / Peti, W.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)71,98610
Polymers71,0032
Non-polymers9838
Water5,801322
1
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0576
Polymers35,5011
Non-polymers5555
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)35,9294
Polymers35,5011
Non-polymers4283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.626, 73.732, 88.123
Angle α, β, γ (deg.)90.000, 104.400, 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

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISHISILEILEchain AAA-3 - 2812 - 286
2METMETMETMETchain BBB-2 - 2823 - 287

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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: 35501.477 Da / Num. of mol.: 2 / Mutation: N193A
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, 330 molecules

#2: Chemical ChemComp-OTA / 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID


Mass: 270.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.0, 0.2 M MgCl2, 17.5% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→28.799 Å / Num. obs: 41762 / % possible obs: 89.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.83 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.112 / Net I/av σ(I): 15.539 / Net I/σ(I): 7.9 / Num. measured all: 145593
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.932.40.266144.7
1.93-1.972.60.245152
1.97-2.012.80.207159.4
2.01-2.052.90.203169.5
2.05-2.0930.197183
2.09-2.143.40.168195.4
2.14-2.193.60.157196.8
2.19-2.253.60.156196.9
2.25-2.323.70.149196.9
2.32-2.393.60.139197.4
2.39-2.483.70.133197.7
2.48-2.583.70.127197.9
2.58-2.73.70.121198.2
2.7-2.843.70.116198.1
2.84-3.023.70.106199.1
3.02-3.253.70.097198.8
3.25-3.583.70.082199.4
3.58-4.093.60.077199.4
4.09-5.163.70.07199.8
5.16-503.60.05199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å28.8 Å
Translation1.9 Å28.8 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C88

1c88


Resolution: 1.9→28.799 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.76
RfactorNum. reflection% reflection
Rfree0.2049 2102 5.04 %
Rwork0.1759 --
obs0.1774 41746 89.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.57 Å2 / Biso mean: 22.5984 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.9→28.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 61 322 4972
Biso mean--24.08 25.47 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044749
X-RAY DIFFRACTIONf_angle_d0.9066401
X-RAY DIFFRACTIONf_chiral_restr0.035681
X-RAY DIFFRACTIONf_plane_restr0.004818
X-RAY DIFFRACTIONf_dihedral_angle_d13.4351808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2747X-RAY DIFFRACTION4.472TORSIONAL
12B2747X-RAY DIFFRACTION4.472TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8962-1.94030.3046820.22741303138545
1.9403-1.98880.2235860.20421653173956
1.9888-2.04250.2131190.1871997211668
2.0425-2.10260.23621080.18732531263986
2.1026-2.17050.22971540.17632881303596
2.1705-2.2480.21561500.17612855300597
2.248-2.3380.21941390.18182848298797
2.338-2.44430.23981430.18032928307197
2.4443-2.57310.23821560.18892886304298
2.5731-2.73420.1721450.19342940308598
2.7342-2.94520.20861620.20022920308299
2.9452-3.24120.23961680.19682927309599
3.2412-3.70930.19911790.16222947312699
3.7093-4.67020.17831730.14729603133100
4.6702-28.80250.16281380.163630683206100

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