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- PDB-2kom: Solution structure of humar Par-3b PDZ2 (residues 451-549) -

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Basic information

Entry
Database: PDB / ID: 2kom
TitleSolution structure of humar Par-3b PDZ2 (residues 451-549)
ComponentsPartitioning defective 3 homolog
KeywordsSIGNALING PROTEIN / Par-3b / PDZ domain / PSI / Structural Genomics / Alternative splicing / Cell cycle / Cell division / Cell junction / Cell membrane / Coiled coil / Cytoplasm / Cytoskeleton / Membrane / Phosphoprotein / Polymorphism / Tight junction / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


internode region of axon / regulation of cellular localization / asymmetric cell division / Tight junction interactions / establishment of centrosome localization / positive regulation of myelination / establishment of epithelial cell polarity / bicellular tight junction assembly / myelination in peripheral nervous system / phosphatidylinositol-3-phosphate binding ...internode region of axon / regulation of cellular localization / asymmetric cell division / Tight junction interactions / establishment of centrosome localization / positive regulation of myelination / establishment of epithelial cell polarity / 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 / 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 / bicellular tight junction / endomembrane system / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / axonogenesis / transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / adherens junction / protein localization / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / cell-cell junction / cell junction / cell cortex / protein-containing complex assembly / protein phosphatase binding / cytoskeleton / cell adhesion / cell cycle / apical plasma membrane / neuronal cell body / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / cytosol
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 speciesHomo sapiens (human)
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: Protein Sci. / Year: 2010
Title: Rapid, robotic, small-scale protein production for NMR screening and structure determination.
Authors: Jensen, D.R. / Woytovich, C. / Li, M. / Duvnjak, P. / Cassidy, M.S. / Frederick, R.O. / Bergeman, L.F. / Peterson, F.C. / Volkman, B.F.
History
DepositionSep 24, 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)13,3941
Polymers13,3941
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 / 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 / CTCL tumor antigen se2- ...PARD-3 / PAR-3 / Atypical PKC isotype-specific-interacting protein / ASIP / CTCL tumor antigen se2-5 / PAR3-alpha


Mass: 13394.235 Da / Num. of mol.: 1 / Fragment: PDZ 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARD3, PAR3, PAR3A / Production host: Escherichia coli (E. coli) / Strain (production host): SG130099[pREP4] / References: UniProt: Q8TEW0

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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)
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] hPar-3 PDZ2, 20 mM sodium phosphate, 50 mM sodium chloride, 90 % H2O, 10 % D2O, 0.02 % sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMhPar-3 PDZ2-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
90 %H2O-41
10 %D2O-51
0.02 %sodium azide-61
Sample conditionsIonic strength: 53 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
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 1318 NOE CONSTRAINTS (351 INTRA, 296 SEQUENTIAL, 178 MEDIUM, AND 520 LONG RANGE) AND 99 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1318 / NOE intraresidue total count: 351 / NOE long range total count: 520 / NOE medium range total count: 178 / NOE sequential total count: 296
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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