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Open data
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Basic information
Entry | Database: PDB / ID: 5uly | |||||||||
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Title | Crystal Structure of Human Protocadherin-15 EC2-3 | |||||||||
![]() | Protocadherin-15 | |||||||||
![]() | Calcium-binding protein / hearing / mechanotransduction / adhesion | |||||||||
Function / homology | ![]() equilibrioception / sensory perception of light stimulus / 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 / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / sensory perception of sound ...equilibrioception / sensory perception of light stimulus / 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 / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / sensory perception of sound / cell-cell junction / cell adhesion / synapse / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wimalasena, L.N. / Sotomayor, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 371.3 KB | Display | ![]() |
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PDB format | ![]() | 304.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tpkC ![]() 5w1dC ![]() 6bwnC ![]() 6bxuC ![]() 6e8fC ![]() 6eb5C ![]() 6eetC ![]() 6mfoC ![]() 6n22C ![]() 6n2eC ![]() 4apxS ![]() 5t4mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _
NCS ensembles :
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Details | Dimer as determined by SEC and AUC |
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Components
#1: Protein | Mass: 29375.723 Da / Num. of mol.: 4 / Fragment: residues 143-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 0.1 M KCl, 15% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: oxford cryo-jet |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 42598 / % possible obs: 96.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.625 |
Reflection shell | Resolution: 2.64→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.7 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4APX, 5T4M Resolution: 2.64→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 21.433 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.288 / 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: 54.895 Å2
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Refinement step | Cycle: 1 / Resolution: 2.64→50 Å
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Refine LS restraints |
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