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- PDB-1v6b: Solution structure of the third PDZ domain of mouse harmonin -

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Basic information

Entry
Database: PDB / ID: 1v6b
TitleSolution structure of the third PDZ domain of mouse harmonin
Componentsharmonin isoform a1
KeywordsPROTEIN BINDING / structural genomics / Usher syndrome / USH1 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


myosin tail binding / protein-containing complex assembly => GO:0065003 / protein localization to microvillus / stereocilia ankle link / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / retinal cone cell development / equilibrioception ...myosin tail binding / protein-containing complex assembly => GO:0065003 / protein localization to microvillus / stereocilia ankle link / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / retinal cone cell development / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / stereocilium / photoreceptor cell maintenance / inner ear morphogenesis / spectrin binding / microvillus / actin filament bundle assembly / brush border / neuromuscular process controlling balance / photoreceptor outer segment / photoreceptor inner segment / sensory perception of sound / G2/M transition of mitotic cell cycle / actin filament binding / apical part of cell / cytoskeleton / synapse / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Harmonin / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsYamada, K. / Nameki, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the third PDZ domain of mouse harmonin
Authors: Yamada, K. / Nameki, N. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionNov 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2004Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: harmonin isoform a1


Theoretical massNumber of molelcules
Total (without water)12,4641
Polymers12,4641
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 harmonin isoform a1


Mass: 12464.007 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 2010016F01 / Plasmid: P020401-47 / References: UniProt: Q9ES64

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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

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Sample preparation

DetailsContents: 20mM Sodium Phosphate buffer, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O
Solvent system: 90% 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6brukercollection
NMRPipe20020425Delglio, F.processing
NMRView5Johnson, B. A.data analysis
CYANA1Guentart, P.structure solution
KUJIRA0.706Kobayashi, N.data analysis
CYANA1Guentart, P.refinement
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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