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- PDB-9cyo: Crystal structure of wild-type human PTP1B (PTPN1) at room temper... -

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Basic information

Entry
Database: PDB / ID: 9cyo
TitleCrystal structure of wild-type human PTP1B (PTPN1) at room temperature (298 K)
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PTP1B / Phosphatase / Allostery / PTP
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to unfolded protein / regulation of signal transduction / growth hormone receptor signaling pathway via JAK-STAT / 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 / negative regulation of MAP kinase activity / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / protein dephosphorylation / ephrin receptor binding / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / endosome lumen / insulin receptor binding / Negative regulation of MET activity / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / 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
BETA-MERCAPTOETHANOL / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsEbrahim, A. / Perdikari, A. / Woods, V.A. / Lawler, K. / Bounds, R. / Singh, N.I. / Mehlman, T. / Riley, B.T. / Sharma, S. / Morris, J.W. ...Ebrahim, A. / Perdikari, A. / Woods, V.A. / Lawler, K. / Bounds, R. / Singh, N.I. / Mehlman, T. / Riley, B.T. / Sharma, S. / Morris, J.W. / Keogh, J.M. / Henning, E. / Smith, M. / Farooqi, I.S. / Keedy, D.A.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
Wellcome Trust207462/Z/17/Z United Kingdom
CitationJournal: Biorxiv / Year: 2024
Title: Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy.
Authors: Perdikari, A. / Woods, V.A. / Ebrahim, A. / Lawler, K. / Bounds, R. / Singh, N.I. / Mehlman, T.S. / Riley, B.T. / Sharma, S. / Morris, J.W. / Keogh, J.M. / Henning, E. / Smith, M. / Farooqi, I.S. / Keedy, D.A.
History
DepositionAug 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4683
Polymers37,3661
Non-polymers1022
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.541, 89.541, 106.212
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

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


Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: catalytic domain
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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.29 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13.5% PEG 8000, 2% ethanol

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.94→43.82 Å / Num. obs: 36906 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 33.36 Å2 / CC1/2: 0.928 / CC star: 0.981 / Rmerge(I) obs: 0.1426 / Rpim(I) all: 0.04832 / Rrim(I) all: 0.1509 / Net I/σ(I): 8.96
Reflection shellResolution: 1.94→2.009 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.884 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 3639 / CC1/2: 0.349 / CC star: 0.72 / Rpim(I) all: 0.9614 / Rrim(I) all: 3.043 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALS3.7.1data reduction
Aimless0.8.2data scaling
MOLREP11phasing
REFMAC5.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→43.82 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.3524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 1814 4.92 %
Rwork0.1695 35084 -
obs0.171 36898 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.35 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 5 104 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252440
X-RAY DIFFRACTIONf_angle_d1.22573297
X-RAY DIFFRACTIONf_chiral_restr0.0636347
X-RAY DIFFRACTIONf_plane_restr0.0099430
X-RAY DIFFRACTIONf_dihedral_angle_d16.7428938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.33081300.30952682X-RAY DIFFRACTION99.86
1.99-2.050.30271710.28862599X-RAY DIFFRACTION100
2.05-2.120.29741340.26932667X-RAY DIFFRACTION99.61
2.12-2.190.27661380.23832684X-RAY DIFFRACTION99.96
2.19-2.280.26161260.20892698X-RAY DIFFRACTION99.96
2.28-2.380.27031470.20722639X-RAY DIFFRACTION99.82
2.38-2.510.23661270.19092705X-RAY DIFFRACTION100
2.51-2.670.21021450.18592703X-RAY DIFFRACTION99.96
2.67-2.870.22011430.18622677X-RAY DIFFRACTION99.89
2.87-3.160.23841340.17942702X-RAY DIFFRACTION99.54
3.16-3.620.16761360.15772724X-RAY DIFFRACTION99.93
3.62-4.560.14391340.12082763X-RAY DIFFRACTION100
4.56-43.820.16511490.1342841X-RAY DIFFRACTION99.07

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