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- PDB-2kbr: Solution structure of harmonin N terminal domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2kbr
TitleSolution structure of harmonin N terminal domain in complex with a internal peptide of cadherin23
Components
  • 18-meric peptide from Cadherin-23
  • HarmoninUSH1C
KeywordsSTRUCTURAL PROTEIN/CELL ADHESION / PROTEIN COMPLEX / Alternative splicing / Coiled coil / Deafness / Hearing / Non-syndromic deafness / Polymorphism / Retinitis pigmentosa / Sensory transduction / Usher syndrome / Vision / Calcium / Cell adhesion / Cell membrane / Disease mutation / Glycoprotein / Membrane / Phosphoprotein / Transmembrane / STRUCTURAL PROTEIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / retinal cone cell development ...protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / response to stimulus / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / spectrin binding / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / brush border / microvillus / actin filament bundle assembly / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / visual perception / photoreceptor inner segment / locomotory behavior / sensory perception of sound / cilium / calcium ion transport / G2/M transition of mitotic cell cycle / apical part of cell / protein-containing complex assembly / cytoskeleton / cadherin binding / centrosome / synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin, N-terminal domain / Harmonin / Paired amphipathic helix 2 (pah2 repeat) / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. ...Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin, N-terminal domain / Harmonin / Paired amphipathic helix 2 (pah2 repeat) / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cadherin-23 / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 20
AuthorsPan, L. / Yan, J. / Wu, L. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Assembling stable hair cell tip link complex via multidentate interactions between harmonin and cadherin 23
Authors: Pan, L. / Yan, J. / Wu, L. / Zhang, M.
History
DepositionDec 5, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Harmonin
B: 18-meric peptide from Cadherin-23


Theoretical massNumber of molelcules
Total (without water)11,7972
Polymers11,7972
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Harmonin / USH1C / Usher syndrome type-1C protein / Autoimmune enteropathy-related antigen AIE-75 / Antigen NY-CO- ...Usher syndrome type-1C protein / Autoimmune enteropathy-related antigen AIE-75 / Antigen NY-CO-38/NY-CO-37 / PDZ-73 protein / Renal carcinoma antigen NY-REN-3


Mass: 9567.099 Da / Num. of mol.: 1 / Fragment: N terminal domain, residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARMONIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6N9
#2: Protein/peptide 18-meric peptide from Cadherin-23 / Otocadherin


Mass: 2230.370 Da / Num. of mol.: 1 / Fragment: internal domein, UNP residues 3182-3200 / Mutation: A107E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Cadherin23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H251

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H COSY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D 1H-15N NOESY
1613D 1H-13C NOESY

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Sample preparation

DetailsContents: 100mM potassium phosphate-1, 1mM DTT-2, 1mM EDTA-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMpotassium phosphate-11
1 mMDTT-21
1 mMEDTA-31
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readchemical shift calculation
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 20

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