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- PDB-1uez: Solution structure of the first PDZ domain of human KIAA1526 protein -

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Basic information

Entry
Database: PDB / ID: 1uez
TitleSolution structure of the first PDZ domain of human KIAA1526 protein
ComponentsKIAA1526 Protein
KeywordsPROTEIN BINDING / PDZ domain / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


paranodal junction maintenance / periciliary membrane compartment / stereocilia ankle link / USH2 complex / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization ...paranodal junction maintenance / periciliary membrane compartment / stereocilia ankle link / USH2 complex / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / retina homeostasis / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / photoreceptor inner segment / ciliary basal body / establishment of localization in cell / actin filament / sensory perception of sound / establishment of protein localization / cilium / growth cone / synapse / positive regulation of gene expression / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Whirlin / : / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Whirlin / : / : / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Kigawa, T. / Muto, Y. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first PDZ domain of human KIAA1526 protein
Authors: Li, H. / Kigawa, T. / Muto, Y. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2003Provider: 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_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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIAA1526 Protein


Theoretical massNumber of molelcules
Total (without water)10,4021
Polymers10,4021
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA1526 Protein


Mass: 10401.824 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA fj04743 / Plasmid: P021030-45 / References: UniProt: Q9P202

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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

DetailsContents: 1.6mM PDZ domain U-15N, 13C; 20mM d-Tris HCl(7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.811Kobayashi, 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 ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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