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- PDB-9cyq: Crystal structure of Q78R mutant human PTP1B (PTPN1) at room temp... -

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Basic information

Entry
Database: PDB / ID: 9cyq
TitleCrystal structure of Q78R mutant 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 / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / mitochondrial crista ...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 / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / mitochondrial crista / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / positive regulation of IRE1-mediated unfolded protein response / negative regulation of vascular associated smooth muscle cell migration / positive regulation of systemic arterial blood pressure / negative regulation of PERK-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / Regulation of IFNA/IFNB signaling / regulation of proteolysis / cellular response to fibroblast growth factor stimulus / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / growth hormone receptor signaling pathway via JAK-STAT / 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 / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of heart rate / endoplasmic reticulum unfolded protein response / negative regulation of insulin receptor signaling pathway / positive regulation of JUN kinase activity / positive regulation of cardiac muscle cell apoptotic process / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / protein tyrosine phosphatase activity / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / 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 MET activity / negative regulation of ERK1 and ERK2 cascade / 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: 2.3 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: 2025
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
Revision 2.0Apr 16, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.year / _citation_author.identifier_ORCID / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id

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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)37,4952
Polymers37,4711
Non-polymers241
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.566, 89.566, 106.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#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: 37470.820 Da / Num. of mol.: 1 / Mutation: Q78R
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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 66.89 %
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: 2.3→43.86 Å / Num. obs: 21897 / % possible obs: 97.99 % / Redundancy: 10.2 % / Biso Wilson estimate: 39.41 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.2756 / Rpim(I) all: 0.09043 / Rrim(I) all: 0.2905 / Net I/σ(I): 5.37
Reflection shellResolution: 2.3→2.386 Å / Redundancy: 10.7 % / Rmerge(I) obs: 3.299 / Mean I/σ(I) obs: 0.37 / Num. unique obs: 2151 / CC1/2: 0.284 / CC star: 0.665 / Rpim(I) all: 1.055 / Rrim(I) all: 3.466 / % possible all: 98.4

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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: 2.3→43.86 Å / SU ML: 0.2368 / Cross valid method: FREE R-VALUE / σ(F): 1.88 / Phase error: 21.9638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 1075 4.92 %
Rwork0.1623 20796 -
obs0.1645 21871 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.26 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 5 61 2382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132420
X-RAY DIFFRACTIONf_angle_d1.22993266
X-RAY DIFFRACTIONf_chiral_restr0.0604346
X-RAY DIFFRACTIONf_plane_restr0.0111424
X-RAY DIFFRACTIONf_dihedral_angle_d6.9454323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.410.31491540.24462550X-RAY DIFFRACTION98.26
2.41-2.540.25851230.21432576X-RAY DIFFRACTION98.43
2.54-2.690.26341190.21842596X-RAY DIFFRACTION98.98
2.69-2.90.25431420.19722590X-RAY DIFFRACTION98.81
2.9-3.190.25481230.20062477X-RAY DIFFRACTION93.96
3.19-3.660.20651440.15822641X-RAY DIFFRACTION99.25
3.66-4.60.15641220.12662661X-RAY DIFFRACTION99.5
4.61-43.860.17251480.13142705X-RAY DIFFRACTION96.97

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