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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 / regulation of macrophage apoptotic process / Tight junction interactions / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of actin filament-based process / phosphatidylinositol phosphate phosphatase activity ...regulation of cellular component size / regulation of macrophage apoptotic process / Tight junction interactions / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of actin filament-based process / phosphatidylinositol phosphate phosphatase activity / 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 / internode region of axon / cellular response to sorbitol / negative regulation of wound healing, spreading of epidermal cells / regulation of cellular localization / phosphatidylinositol-3-phosphate phosphatase activity / regulation of Fc receptor mediated stimulatory signaling pathway / central nervous system neuron axonogenesis / negative regulation of dendrite extension / negative regulation of defense response to bacterium / PAR polarity complex / postsynaptic density assembly / apical constriction / negative regulation of dendritic spine morphogenesis / neuron-neuron synaptic transmission / inositol phosphate catabolic process / protein tyrosine/serine/threonine phosphatase activity / cellular response to decreased oxygen levels / presynaptic membrane assembly / synapse maturation / negative regulation of axon regeneration / establishment of centrosome localization / negative regulation of cell cycle G1/S phase transition / cellular response to electrical stimulus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of myelination / establishment of epithelial cell polarity / negative regulation of ribosome biogenesis / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / positive regulation of myelination / myelin sheath adaxonal region / lateral loop / negative regulation of cardiac muscle cell proliferation / negative regulation of organ growth / negative regulation of androgen receptor signaling pathway / negative regulation of excitatory postsynaptic potential / forebrain morphogenesis / regulation of B cell apoptotic process / negative regulation of focal adhesion assembly / regulation of axon regeneration / phosphatidylinositol dephosphorylation / bicellular tight junction assembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / anaphase-promoting complex binding / Schmidt-Lanterman incisure / prostate gland growth / dentate gyrus development / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of peptidyl-threonine phosphorylation / myelination in peripheral nervous system / ubiquitin ligase activator activity / dendritic spine morphogenesis / cellular response to leptin stimulus / negative regulation of cell size / maternal behavior / phosphatidylinositol-3-phosphate binding / response to arsenic-containing substance / spindle assembly involved in female meiosis / brain morphogenesis / platelet-derived growth factor receptor binding / cellular response to ethanol / positive regulation of ubiquitin-dependent protein catabolic process / protein targeting to membrane / cardiac muscle tissue development / long-term synaptic depression / wound healing, spreading of cells / centrosome localization / negative regulation of epithelial to mesenchymal transition / negative regulation of phagocytosis / apical junction complex / protein serine/threonine phosphatase activity / cellular response to insulin-like growth factor stimulus / response to zinc ion / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / response to ATP / male mating behavior / protein-serine/threonine phosphatase / negative regulation of G1/S transition of mitotic cell cycle
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / : / : / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / : / : / Inositol hexakisphosphate / 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 / Polymorphic toxin system, DSP-PTPase phosphatase / 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 / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / 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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