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Yorodumi- PDB-6n2e: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n2e | ||||||
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Title | Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E | ||||||
Components |
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Keywords | CELL ADHESION / Mechanotransduction / Calcium-binding protein / stereocilia / hair cell / tip link | ||||||
Function / homology | Function and homology information cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / 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 / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Choudhary, D. / De-la-Torre, P. / Sotomayor, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. Authors: Choudhary, D. / Narui, Y. / Neel, B.L. / Wimalasena, L.N. / Klanseck, C.F. / De-la-Torre, P. / Chen, C. / Araya-Secchi, R. / Tamilselvan, E. / Sotomayor, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n2e.cif.gz | 452.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n2e.ent.gz | 372.7 KB | Display | PDB format |
PDBx/mmJSON format | 6n2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/6n2e ftp://data.pdbj.org/pub/pdb/validation_reports/n2/6n2e | HTTPS FTP |
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-Related structure data
Related structure data | 5tpkC 5ulyC 5w1dC 6bwnC 6bxuC 6e8fC 6eb5C 6eetC 6mfoSC 6n22C 4aq8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43069.160 Da / Num. of mol.: 2 / Mutation: G16D, N369D, Q370N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: A0A087X1T6, UniProt: Q96QU1*PLUS #2: Protein | Mass: 23884.445 Da / Num. of mol.: 2 / Mutation: T15E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99PF4 #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Imidazole pH 6.8, 46% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 41847 / % possible obs: 93.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.055 / Net I/σ(I): 12.33 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4.4 % / Num. unique obs: 1806 / Rpim(I) all: 0.236 / % possible all: 86.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MFO, 4AQ8 Resolution: 2.9→49.52 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.739 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.813 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→49.52 Å
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