[English] 日本語
![](img/lk-miru.gif)
- PDB-6n2e: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6n2e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E | ||||||
![]() |
| ||||||
![]() | CELL ADHESION / Mechanotransduction / Calcium-binding protein / stereocilia / hair cell / tip link | ||||||
Function / homology | ![]() cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / 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 ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / 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 / 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 / cell-cell junction / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Choudhary, D. / De-la-Torre, P. / Sotomayor, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 452.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 372.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 474 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() #2: Protein | Mass: 23884.445 Da / Num. of mol.: 2 / Mutation: T15E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.08 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→49.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|