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Yorodumi- PDB-2kbr: Solution structure of harmonin N terminal domain in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kbr | ||||||
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Title | Solution structure of harmonin N terminal domain in complex with a internal peptide of cadherin23 | ||||||
Components |
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Keywords | STRUCTURAL 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 / response to stimulus / 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 / 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 / G2/M transition of mitotic cell cycle / calcium ion transport / apical part of cell / protein-containing complex assembly / cytoskeleton / cadherin binding / centrosome / synapse / calcium ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 20 | ||||||
Authors | Pan, L. / Yan, J. / Wu, L. / Zhang, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kbr.cif.gz | 641.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kbr.ent.gz | 537.5 KB | Display | PDB format |
PDBx/mmJSON format | 2kbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kbr_validation.pdf.gz | 355.3 KB | Display | wwPDB validaton report |
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Full document | 2kbr_full_validation.pdf.gz | 632.6 KB | Display | |
Data in XML | 2kbr_validation.xml.gz | 36 KB | Display | |
Data in CIF | 2kbr_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/2kbr ftp://data.pdbj.org/pub/pdb/validation_reports/kb/2kbr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein/peptide | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 100mM potassium phosphate-1, 1mM DTT-2, 1mM EDTA-3, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 20 |