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- PDB-2dle: Solution structure of the fourth fn3 domain of human receptor-typ... -

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Basic information

Entry
Database: PDB / ID: 2dle
TitleSolution structure of the fourth fn3 domain of human receptor-type tyrosine-protein phosphatase eta
ComponentsReceptor-type tyrosine-protein phosphatase eta
KeywordsHYDROLASE / Protein-tyrosine phosphatase eta / R-PTP-eta / HPTP eta / Protein-tyrosine phosphatase receptor type J / Density-enhanced phosphatase 1 / CD148 antigen / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / positive regulation of platelet activation / negative regulation of vascular permeability / platelet-derived growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / platelet formation ...positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / positive regulation of platelet activation / negative regulation of vascular permeability / platelet-derived growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / platelet formation / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of macrophage chemotaxis / Phosphorylation of CD3 and TCR zeta chains / negative regulation of epidermal growth factor receptor signaling pathway / oligodendrocyte differentiation / phosphatase activity / peptidyl-tyrosine dephosphorylation / platelet-derived growth factor receptor signaling pathway / immunological synapse / positive regulation of focal adhesion assembly / negative regulation of MAP kinase activity / regulation of cell adhesion / vasculogenesis / specific granule membrane / positive regulation of phagocytosis / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / Negative regulation of FLT3 / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / positive regulation of cell adhesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / B cell differentiation / positive regulation of calcium-mediated signaling / axon guidance / negative regulation of cell migration / negative regulation of cell growth / cytokine-mediated signaling pathway / Negative regulation of MET activity / beta-catenin binding / ruffle membrane / positive regulation of tumor necrosis factor production / blood coagulation / cell junction / glucose homeostasis / cell-cell junction / T cell receptor signaling pathway / heart development / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / nuclear body / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / nucleolus / cell surface / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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. ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIzumi, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the fourth fn3 domain of human receptor-type tyrosine-protein phosphatase eta
Authors: Izumi, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase eta


Theoretical massNumber of molelcules
Total (without water)10,7471
Polymers10,7471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase eta / Protein-tyrosine phosphatase eta / R-PTP-eta / HPTP eta / Protein-tyrosine phosphatase receptor ...Protein-tyrosine phosphatase eta / R-PTP-eta / HPTP eta / Protein-tyrosine phosphatase receptor type J / Density-enhanced phosphatase 1 / DEP-1 / CD148 antigen


Mass: 10746.783 Da / Num. of mol.: 1 / Fragment: fn3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: PTPRJ, DEP1 / Plasmid: P050302-39 / Production host: Cell free synthesis / References: UniProt: Q12913, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.05mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.Adata analysis
KUJIRA0.932Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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