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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


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 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 / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / regulation of actin filament-based process / rhythmic synaptic transmission / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / : / PAR polarity complex / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / negative regulation of dendritic spine morphogenesis / 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 / : / negative regulation of ribosome biogenesis / negative regulation of axonogenesis / Ub-specific processing proteases / negative regulation of myelination / response to xenobiotic stimulus => GO:0009410 / myelin sheath adaxonal region / positive regulation of myelination / lateral loop / establishment of epithelial cell polarity / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of cardiac muscle cell proliferation / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / protein tyrosine/serine/threonine phosphatase activity / forebrain morphogenesis / regulation of B cell apoptotic process / negative regulation of focal adhesion assembly / Schmidt-Lanterman incisure / negative regulation of epithelial to mesenchymal transition / regulation of axon regeneration / phosphatidylinositol dephosphorylation / prostate gland growth / anaphase-promoting complex binding / myelination in peripheral nervous system / bicellular tight junction assembly / maternal behavior / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / positive regulation of ubiquitin-dependent protein catabolic process / phosphatidylinositol-3-phosphate binding / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of cell size / cellular response to leptin stimulus / response to arsenic-containing substance / cardiac muscle tissue development / brain morphogenesis / platelet-derived growth factor receptor binding / cellular response to ethanol / negative regulation of phagocytosis / protein targeting to membrane / long-term synaptic depression / wound healing, spreading of cells / cellular response to insulin-like growth factor stimulus / centrosome localization / apical junction complex / regulation of synaptic transmission, GABAergic / adult behavior / male mating behavior / protein serine/threonine phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / response to ATP / establishment of cell polarity / response to zinc ion / ubiquitin-specific protease binding / protein-serine/threonine phosphatase / regulation of neuron projection development
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 / Dual specificity phosphatase, catalytic domain ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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: 6.0 / 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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