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- PDB-6gbe: Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Pepti... -

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Basic information

Entry
Database: PDB / ID: 6gbe
TitleMurine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex
Components
  • Serine/threonine-protein kinase N2
  • Tyrosine-protein phosphatase non-receptor type 13
KeywordsPROTEIN BINDING / PTPN13 / PDZ3
Function / homology
Function and homology information


RND3 GTPase cycle / negative regulation of excitatory synapse assembly / epithelial cell migration / RND2 GTPase cycle / RND1 GTPase cycle / protein kinase C / Synthesis of PIPs at the plasma membrane / diacylglycerol-dependent serine/threonine kinase activity / cell projection organization / phosphatidylinositol 3-kinase regulatory subunit binding ...RND3 GTPase cycle / negative regulation of excitatory synapse assembly / epithelial cell migration / RND2 GTPase cycle / RND1 GTPase cycle / protein kinase C / Synthesis of PIPs at the plasma membrane / diacylglycerol-dependent serine/threonine kinase activity / cell projection organization / phosphatidylinositol 3-kinase regulatory subunit binding / apical junction assembly / regulation of cell motility / RNA polymerase binding / intermediate filament cytoskeleton / apical junction complex / RHOB GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RHOC GTPase cycle / positive regulation of cytokinesis / cleavage furrow / RHOA GTPase cycle / positive regulation of viral genome replication / dephosphorylation / RHO GTPases activate PKNs / RAC1 GTPase cycle / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / fibrillar center / small GTPase binding / histone deacetylase binding / lamellipodium / cell body / kinase activity / midbody / nuclear body / cytoskeleton / cell adhesion / protein kinase activity / intracellular signal transduction / cadherin binding / cell cycle / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / signal transduction / protein-containing complex / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain ...Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / HR1 rho-binding domain / REM-1 domain profile. / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / Protein kinase, C-terminal / Protein kinase C terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 domain / Tyrosine specific protein phosphatases domain profile. / C2 domain superfamily / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase N2 / Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKock, G. / Stoll, R.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Molecular Basis of Class III Ligand Recognition by PDZ3 in Murine Protein Tyrosine Phosphatase PTPN13.
Authors: Kock, G. / Dicks, M. / Yip, K.T. / Kohl, B. / Putz, S. / Heumann, R. / Erdmann, K.S. / Stoll, R.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Category: database_2 / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 13
B: Serine/threonine-protein kinase N2


Theoretical massNumber of molelcules
Total (without water)14,2732
Polymers14,2732
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area820 Å2
ΔGint-5 kcal/mol
Surface area10110 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 13 / PTP36 / Protein tyrosine phosphatase DPZPTP / Protein tyrosine phosphatase PTP-BL / Protein- ...PTP36 / Protein tyrosine phosphatase DPZPTP / Protein tyrosine phosphatase PTP-BL / Protein-tyrosine phosphatase RIP


Mass: 12690.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptpn13, Ptp14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64512, protein-tyrosine-phosphatase
#2: Protein/peptide Serine/threonine-protein kinase N2 / PKN gamma / Protein kinase C-like 2 / Protein-kinase C-related kinase 2


Mass: 1582.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16513, protein kinase C

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
151isotropic13D (H)CCH-TOCSY
131isotropic12D 1H-1H NOESY
142isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution20.5 mM [U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMPDZ3/PRK2[U-99% 13C; U-99% 15N]1
0.5 mMPDZ3/PRK2[U-99% 15N]2
Sample conditionsIonic strength: PBS Not defined / Label: conditions_1 / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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