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- PDB-2lc7: Solution structure of the isolated Par-6 PDZ domain -

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Basic information

Entry
Database: PDB / ID: 2lc7
TitleSolution structure of the isolated Par-6 PDZ domain
ComponentsPar-6
KeywordsCELL ADHESION / CRIB / allostery / cell polarity
Function / homology
Function and homology information


CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity / RHOU GTPase cycle ...CDC42 GTPase cycle / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / establishment of neuroblast polarity / RHOU GTPase cycle / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Asymmetric localization of PCP proteins / establishment or maintenance of polarity of embryonic epithelium / muscle cell postsynaptic specialization / border follicle cell migration / asymmetric neuroblast division / morphogenesis of a polarized epithelium / apical cortex / apical protein localization / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of smoothened signaling pathway / centrosome cycle / positive regulation of filopodium assembly / protein kinase inhibitor activity / bicellular tight junction / positive regulation of lamellipodium assembly / synapse assembly / terminal bouton / cell cortex / apical plasma membrane / plasma membrane
Similarity search - Function
Partitioning defective protein 6, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Partitioning defective protein 6, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsVolkman, B.F. / Whitney, D.S. / Peterson, F.C.
CitationJournal: Structure / Year: 2011
Title: A Conformational Switch in the CRIB-PDZ Module of Par-6.
Authors: Whitney, D.S. / Peterson, F.C. / Volkman, B.F.
History
DepositionApr 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Par-6


Theoretical massNumber of molelcules
Total (without water)10,9261
Polymers10,9261
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 Par-6 / PAR-6 / LD29223p


Mass: 10926.463 Da / Num. of mol.: 1 / Fragment: sequence database residues 156-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG5884, Dmel_CG5884, par-6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O97111

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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] Par-6, 20 mM sodium phosphate, 50 mM potassium chloride, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPar-6-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMpotassium chloride-31
Sample conditionsIonic strength: 53 / pH: 5.5 / 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
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.structure solution
CYANAGuntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE ...Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE BASED ON A TOTAL OF 1412 NOE CONSTRAINTS ( 393 INTRA, 351 SEQUENTIAL, 211 MEDIUM, AND 457 LONG RANGE) AND 130 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS., STRUCTURES ARE BASED ON A TOTAL OF 1423 NOE CONSTRAINTS ( 388 INTRA, 355 SEQUENTIAL, 210 MEDIUM, AND 470 LONG RANGE) AND 130 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1412 / NOE intraresidue total count: 393 / NOE long range total count: 457 / NOE medium range total count: 211 / NOE sequential total count: 351 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 67
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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