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- PDB-2k20: Solution structure of Par-3 PDZ3 in complex with PTEN peptide -

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Basic information

Entry
Database: PDB / ID: 2k20
TitleSolution structure of Par-3 PDZ3 in complex with PTEN peptide
Components
  • Partitioning-defective 3 homolog
  • Protein tyrosine phosphatase and tensin homolog
KeywordsSIGNALING PROTEIN / Par-3 / PTEN / PDZ domain / Scaffold protein / Cell polarity / Alternative splicing / Cell cycle / Cell division / Cell junction / Coiled coil / Membrane / Phosphoprotein / Tight junction
Function / homology
Function and homology information


regulation of cellular component size / Negative regulation of the PI3K/AKT network / positive regulation of TRAIL-activated apoptotic signaling pathway / : / Synthesis of PIPs at the plasma membrane / Downstream TCR signaling / Ovarian tumor domain proteases / Tight junction interactions / Regulation of PTEN localization / regulation of myeloid cell apoptotic process ...regulation of cellular component size / Negative regulation of the PI3K/AKT network / positive regulation of TRAIL-activated apoptotic signaling pathway / : / Synthesis of PIPs at the plasma membrane / Downstream TCR signaling / Ovarian tumor domain proteases / Tight junction interactions / Regulation of PTEN localization / regulation of myeloid cell apoptotic process / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / : / internode region of axon / Regulation of PTEN stability and activity / regulation of cellular localization / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol-3-phosphate phosphatase activity / : / central nervous system neuron axonogenesis / PAR polarity complex / postsynaptic density assembly / negative regulation of dendritic spine morphogenesis / neuron-neuron synaptic transmission / apical constriction / negative regulation of potassium ion transmembrane transporter activity / cellular response to decreased oxygen levels / presynaptic membrane assembly / synapse maturation / negative regulation of axon regeneration / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / : / establishment of centrosome localization / Ub-specific processing proteases / protein tyrosine/serine/threonine phosphatase activity / negative regulation of myelination / response to xenobiotic stimulus => GO:0009410 / negative regulation of ribosome biogenesis / negative regulation of axonogenesis / lateral loop / negative regulation of cardiac muscle cell proliferation / positive regulation of myelination / myelin sheath adaxonal region / establishment of epithelial cell polarity / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / regulation of B cell apoptotic process / regulation of axon regeneration / Schmidt-Lanterman incisure / anaphase-promoting complex binding / bicellular tight junction assembly / phosphatidylinositol dephosphorylation / myelination in peripheral nervous system / prostate gland growth / negative regulation of cyclin-dependent protein serine/threonine kinase activity / dentate gyrus development / positive regulation of ubiquitin protein ligase activity / maternal behavior / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell size / phosphatidylinositol-3-phosphate binding / cellular response to leptin stimulus / response to arsenic-containing substance / dendritic spine morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / platelet-derived growth factor receptor binding / brain morphogenesis / negative regulation of epithelial to mesenchymal transition / cellular response to ethanol / cardiac muscle tissue development / protein targeting to membrane / long-term synaptic depression / negative regulation of phagocytosis / wound healing, spreading of cells / apical junction complex / cellular response to insulin-like growth factor stimulus / centrosome localization / regulation of synaptic transmission, GABAergic / negative regulation of G1/S transition of mitotic cell cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to ATP / establishment of cell polarity / protein serine/threonine phosphatase activity / adult behavior / male mating behavior / response to zinc ion / protein-serine/threonine phosphatase / ubiquitin-specific protease binding
Similarity search - Function
: / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein ...: / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / PDZ domain / Pdz3 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-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Partitioning defective 3 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Wu, H. / Chan, L. / Zhang, M.
CitationJournal: To be Published
Title: Solution structure of Par-3 PDZ3 in complex with PTEN peptide
Authors: Feng, W. / Wu, H. / Chan, L. / Zhang, M.
History
DepositionMar 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 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: Partitioning-defective 3 homolog
B: Protein tyrosine phosphatase and tensin homolog


Theoretical massNumber of molelcules
Total (without water)12,4442
Polymers12,4442
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 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Partitioning-defective 3 homolog / PARD-3 / PAR-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific- ...PARD-3 / PAR-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific-binding protein / ASBP


Mass: 11142.648 Da / Num. of mol.: 1 / Fragment: PDZ 3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pard3, Par3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z340
#2: Protein/peptide Protein tyrosine phosphatase and tensin homolog / Protein tyrosine phosphatase and tensin-like protein


Mass: 1301.359 Da / Num. of mol.: 1 / Fragment: UNP residues 393-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pten, PTEN/MMAC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O54857

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1223D 1H-15N NOESY
1333D HN(CA)CB
1433D CBCA(CO)NH
1533D HNCO
1643D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Par-3 PDZ3/PTEN peptide, 100% D2O100% D2O
21 mM [U-100% 15N] Par-3 PDZ3/PTEN peptide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] Par-3 PDZ3/PTEN peptide, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] Par-3 PDZ3/PTEN peptide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPar-3 PDZ3/PTEN peptide1
1 mMPar-3 PDZ3/PTEN peptide[U-100% 15N]2
1 mMPar-3 PDZ3/PTEN peptide[U-100% 13C; U-100% 15N]3
1 mMPar-3 PDZ3/PTEN peptide[U-100% 13C; U-100% 15N]4
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: ambient atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PIPPGarrettdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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