+Open data
-Basic information
Entry | Database: PDB / ID: 5w1d | |||||||||
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Title | Crystal Structure of Mouse Protocadherin-15 EC4-7 | |||||||||
Components | Protocadherin-15 | |||||||||
Keywords | CELL ADHESION / Hearing / Mechanotransduction / Adhesion / Calcium-binding protein | |||||||||
Function / homology | Function and homology information detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / photoreceptor cell maintenance ...detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / photoreceptor cell maintenance / adult walking behavior / auditory receptor cell stereocilium organization / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / visual perception / locomotory behavior / actin filament organization / morphogenesis of an epithelium / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / synapse / calcium ion binding / extracellular space / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | |||||||||
Authors | Klanseck, C.F. / Neel, B.L. / Sotomayor, M. | |||||||||
Funding support | United States, 2items
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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 | 5w1d.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w1d.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 5w1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w1d ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w1d | HTTPS FTP |
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-Related structure data
Related structure data | 5tpkSC 5ulyC 6bwnC 6bxuC 6e8fC 6eb5C 6eetC 6mfoC 6n22C 6n2eC 5t4mS 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: 47121.254 Da / Num. of mol.: 1 / Fragment: residues 401-818 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99PJ1 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density % sol: 74.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 2.0 M MgAc 23% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→76.09 Å / Num. obs: 14064 / % possible obs: 98.5 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 3.35→3.41 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 596 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5t4m, 5tpk Resolution: 3.35→76.09 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU B: 56.847 / SU ML: 0.372 / Cross valid method: THROUGHOUT / ESU R: 1.744 / ESU R Free: 0.466 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.669 Å2
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Refinement step | Cycle: 1 / Resolution: 3.35→76.09 Å
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Refine LS restraints |
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