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- PDB-1x5z: Solution structure of the fibronectin type-III domain of human pr... -

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Entry
Database: PDB / ID: 1x5z
TitleSolution structure of the fibronectin type-III domain of human protein tyrosine phosphatase, receptor type, D isoform 4 variant
ComponentsReceptor-type tyrosine-protein phosphatase delta
KeywordsHYDROLASE / Fibronectin type III domain containing protein / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / presynapse assembly / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / presynapse assembly / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / phosphate-containing compound metabolic process / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / cellular response to hypoxia / signaling receptor binding / glutamatergic synapse / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYoneyama, M. / Saito, K. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the fibronectin type-III domain of human protein tyrosine phosphatase, receptor type, D isoform 4 variant
Authors: Yoneyama, M. / Saito, K. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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 delta


Theoretical massNumber of molelcules
Total (without water)12,2721
Polymers12,2721
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 delta / Protein-tyrosine phosphatase delta / R-PTP-delta / Protein tyrosine phosphatase / receptor type / D isoform 4


Mass: 12272.406 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PTPRD / Plasmid: P050131-05 / References: UniProt: P23468, 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: 1.37mM fn3 domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, 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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