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

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Basic information

Entry
Database: PDB / ID: 2lsr
TitleSolution structure of harmonin N terminal domain in complex with a exon68 encoded peptide of cadherin23
Components
  • HarmoninUSH1C
  • peptide from Cadherin-23
KeywordsStructural Protein/cell Adhesion / protein complex / usher syndrome / 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 / membrane => GO:0016020 / cytoskeleton / cadherin binding / centrosome / synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cadherin-23 / 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 ...Cadherin-23 / 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 / Cadherin-23 / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsPan, L. / Wu, L. / Zhang, C. / Zhang, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Large protein assemblies formed by multivalent interactions between cadherin23 and harmonin suggest a stable anchorage structure at the tip link of stereocilia.
Authors: Wu, L. / Pan, L. / Zhang, C. / Zhang, M.
History
DepositionMay 4, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,4752
Polymers11,4752
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 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 9567.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIE75, USH1C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Y6N9
#2: Protein/peptide peptide from Cadherin-23 /


Mass: 1908.287 Da / Num. of mol.: 1 / Fragment: exon68 encoded peptide / Mutation: V103E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH23, Ush1D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: F6U049, UniProt: Q9H251*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY aliphatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.6 mM [U-99% 13C; U-99% 15N] protein_1-1, 0.6 mM [U-99% 13C; U-99% 15N] protein_2-2, 100 mM potassium phosphate-3, 1 mM DTT-4, 1 mM EDTA-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMprotein_1-1[U-99% 13C; U-99% 15N]1
0.6 mMprotein_2-2[U-99% 13C; U-99% 15N]1
100 mMpotassium phosphate-31
1 mMDTT-41
1 mMEDTA-51
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 Readstructure solution
PIPPGarrettchemical shift assignment
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1695 / NOE intraresidue total count: 670 / NOE long range total count: 277 / NOE medium range total count: 362 / NOE sequential total count: 386 / Hydrogen bond constraints total count: 88 / Protein phi angle constraints total count: 69 / Protein psi angle constraints total count: 69
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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