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- PDB-1va8: Solution structure of the PDZ domain of Pals1 protein -

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Basic information

Entry
Database: PDB / ID: 1va8
TitleSolution structure of the PDZ domain of Pals1 protein
ComponentsMAGUK p55 subfamily member 5
KeywordsMEMBRANE PROTEIN / PDZ domain / palmitoylated 5 / Pals1 protein / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein localization to myelin sheath abaxonal region / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / guanylate kinase activity / plasma membrane organization / lateral loop / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / Schmidt-Lanterman incisure ...protein localization to myelin sheath abaxonal region / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / guanylate kinase activity / plasma membrane organization / lateral loop / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / Schmidt-Lanterman incisure / peripheral nervous system myelin maintenance / establishment or maintenance of epithelial cell apical/basal polarity / generation of neurons / central nervous system neuron development / bicellular tight junction / protein localization to plasma membrane / adherens junction / protein localization / cerebral cortex development / apical part of cell / gene expression / perikaryon / apical plasma membrane / protein domain specific binding / axon / Golgi apparatus / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
L27-N / MPP5, SH3 domain / L27_N / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site ...L27-N / MPP5, SH3 domain / L27_N / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.-R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PDZ domain of Pals1 protein
Authors: Qin, X.-R. / Hayashi, F. / Yokoyama, S.
History
DepositionFeb 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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 / _struct_ref_seq_dif.details
Revision 1.4Dec 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: MAGUK p55 subfamily member 5


Theoretical massNumber of molelcules
Total (without water)11,9501
Polymers11,9501
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 / 100
RepresentativeModel #1lowest energy

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Components

#1: Protein MAGUK p55 subfamily member 5 / Pals1 protein / Protein associated with Lin-7 1


Mass: 11950.371 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: RIKEN cDNA 3830420B02 / Plasmid: P030203-38 / References: UniProt: Q9JLB2

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Experimental details

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Experiment

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

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Sample preparation

Details
Solution-IDContents
11.05mM 13C, 15N-labeled protein; 20mM PiNa(pH6.0); 100mM NaCl; 1mMd10-DTT; 0.02% NaN3
290%H2O; 10%D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio.F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.854Kobayashi,N.data analysis
CYANA1.0.7Guentert,P.structure solution
CYANA1.0.7Guentert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 20

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