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- PDB-2ogp: Solution structure of the second PDZ domain of Par-3 -

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Basic information

Entry
Database: PDB / ID: 2ogp
TitleSolution structure of the second PDZ domain of Par-3
ComponentsPartitioning-defective 3 homolog
KeywordsSIGNALING PROTEIN / cell polarity / Par-3 / PDZ domain
Function / homology
Function and homology information


Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / establishment of centrosome localization / lateral loop / positive regulation of myelination ...Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / establishment of centrosome localization / lateral loop / positive regulation of myelination / establishment of epithelial cell polarity / Schmidt-Lanterman incisure / bicellular tight junction assembly / myelination in peripheral nervous system / phosphatidylinositol-3-phosphate binding / establishment or maintenance of epithelial cell apical/basal polarity / protein targeting to membrane / wound healing, spreading of cells / centrosome localization / apical junction complex / establishment of cell polarity / negative regulation of peptidyl-threonine phosphorylation / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / bicellular tight junction / endomembrane system / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / adherens junction / protein localization / microtubule cytoskeleton organization / spindle / cell-cell junction / apical part of cell / cell junction / cell cortex / protein phosphatase binding / cell adhesion / cell cycle / apical plasma membrane / cell division / neuronal cell body / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / PDZ domain / Pdz3 Domain / 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
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. / Chen, J. / Chan, L.-N. / Zhang, M.
CitationJournal: Mol.Cell / Year: 2007
Title: PDZ domains of par-3 as potential phosphoinositide signaling integrators
Authors: Wu, H. / Feng, W. / Chen, J. / Chan, L.-N. / Huang, S. / Zhang, M.
History
DepositionJan 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 27, 2023Group: 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


Theoretical massNumber of molelcules
Total (without water)10,4661
Polymers10,4661
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: 10466.090 Da / Num. of mol.: 1 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z340

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
133HNCO
143HN(CA)CB
153CBCA(CO)NH
1643D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM unlabelled Par-3 PDZ2; 100mM potassium phosphate; 99.9% D2O99.9% D2O
21.5mM uniformly 15N labelled Par-3 PDZ2; 100mM potassium phosphate; 90% H2O, 10% D2O90% H2O/10% D2O
31.5mM uniformly 15N/13C labelled Par-3 PDZ2; 100mM potassium phosphate; 90% H2O, 10% D2O90% H2O/10% D2O
41.5mM uniformly 15N/13C labelled Par-3 PDZ2; 100mM potassium phosphate; 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 6.5 / Pressure: 1 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
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
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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