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- PDB-2koj: Solution structure of mouse Par-3 PDZ2 (residues 450-558) -

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Basic information

Entry
Database: PDB / ID: 2koj
TitleSolution structure of mouse Par-3 PDZ2 (residues 450-558)
ComponentsPartitioning defective 3 homolog
KeywordsSIGNALING PROTEIN / Par-3 / PDZ domain / structural genomics / Alternative splicing / Cell cycle / Cell division / Cell junction / Coiled coil / Cytoplasm / Cytoskeleton / Membrane / Phosphoprotein / Tight junction / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


Tight junction interactions / regulation of actin filament-based process / internode region of axon / regulation of cellular localization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / apical constriction / establishment of centrosome localization / lateral loop / positive regulation of myelination / establishment of epithelial cell polarity ...Tight junction interactions / regulation of actin filament-based process / internode region of axon / regulation of cellular localization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 or maintenance of cell polarity / 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 / cell-cell adhesion / spindle / cell-cell junction / cell junction / cell cortex / protein phosphatase binding / cell adhesion / apical plasma membrane / cell cycle / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model detailslowest energy, model 1
AuthorsVolkman, B.F. / Tyler, R.C. / Peterson, F.C. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structural Bioinformatics, 2nd edition / Year: 2009
Title: Macromolecular Structure Determination by NMR Sepectroscopy
Authors: Markley, J.L. / Bahrami, A. / Eghbalnia, H.R. / Peterson, F.C. / Ulrich, E.L. / Westler, W.M. / Volkman, B.F.
History
DepositionSep 23, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 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


Theoretical massNumber of molelcules
Total (without water)12,0451
Polymers12,0451
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Partitioning defective 3 homolog / PARD-3 / PAR-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Ephrin-interacting protein / PHIP


Mass: 12044.837 Da / Num. of mol.: 1 / Fragment: PDZ 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Par-3, Par3, Pard3 / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[pREP4] / References: UniProt: Q99NH2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] mPar3 PDZ2, 20 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMmPar3 PDZ2-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.02 %sodium azide-41
Sample conditionsIonic strength: 54 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1307 NOE CONSTRAINTS (219 INTRA, 388 SEQUENTIAL, 209 MEDIUM, AND 491 LONG RANGE) AND 117 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1307 / NOE intraresidue total count: 219 / NOE long range total count: 491 / NOE medium range total count: 209 / NOE sequential total count: 388
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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