+Open data
-Basic information
Entry | Database: PDB / ID: 1x5n | ||||||
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Title | Solution structure of the second PDZ domain of harmonin protein | ||||||
Components | HarmoninUSH1C | ||||||
Keywords | STRUCTURAL PROTEIN / PDZ domain / Harmonin / Usher syndrome 1C protein / Autoimmune enteropathy-related antigen AIE-75 / Antigen NY-CO-38/NY-CO-37 / PDZ-73 protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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 / retinal cone cell development / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization ...protein localization to microvillus / 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 / 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 / actin filament bundle assembly / microvillus / brush border / photoreceptor outer segment / photoreceptor inner segment / sensory perception of sound / cilium / G2/M transition of mitotic cell cycle / apical part of cell / protein-containing complex assembly / cytoskeleton / synapse / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the second PDZ domain of harmonin protein Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x5n.cif.gz | 637.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x5n.ent.gz | 552.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/1x5n ftp://data.pdbj.org/pub/pdb/validation_reports/x5/1x5n | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11698.110 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: USH1C; AIE75 / Plasmid: p040510-04 / References: UniProt: Q9Y6N9 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.13mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |