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- PDB-1ry4: NMR Structure of the CRIB-PDZ module of Par-6 -

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Basic information

Entry
Database: PDB / ID: 1ry4
TitleNMR Structure of the CRIB-PDZ module of Par-6
ComponentsCG5884-PA
KeywordsCELL ADHESION / PDZ / CRIB / Cdc-42 / Cell Polarization / Polarity adaptor complex
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
AuthorsPeterson, F.C. / Penkert, R.R. / Volkman, B.F. / Prehoda, K.E.
CitationJournal: Mol.Cell / Year: 2004
Title: Cdc42 Regulates the Par-6 PDZ Domain through an Allosteric CRIB-PDZ Transition.
Authors: Peterson, F.C. / Penkert, R.R. / Volkman, B.F. / Prehoda, K.E.
History
DepositionDec 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG5884-PA


Theoretical massNumber of molelcules
Total (without water)13,7601
Polymers13,7601
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 #3closest to the average

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Components

#1: Protein CG5884-PA


Mass: 13759.750 Da / Num. of mol.: 1 / Fragment: CRIB-PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Par-6 / Plasmid: pBH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 18860099, UniProt: O97111*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1313D 13C-separated aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Par-6 U-15C,13C, 20mM phosphate buffer, 0.05% sodium azide90% H2O/10% D2O
20.5mM Par-6 U-15, 20mM phosphate buffer, 0.05% sodium azide90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium chloride / pH: 5.5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Bruker Instrumentscollection
NMRPipe97.027.12.56Frank Delaglioprocessing
XEASY1.3.13Christian Bartelsdata analysis
GARANT2.1Christian Bartelsdata analysis
CYANA1.0.6Peter Guntertstructure solution
XPLOR-NIH2.0.6Axel Brunger and Marius Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1703 restraints, 1564 are NOE-derived distance constraints, 139 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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