[English] 日本語
![](img/lk-miru.gif)
- PDB-6mfo: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6mfo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N | ||||||
![]() | Protocadherin-15 | ||||||
![]() | CELL ADHESION / Mechanotransduction / Calcium-binding protein / stereocilia / hair cell / tip link | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Choudhary, D. / 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 | ![]() | 149.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 116.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tpkC ![]() 5ulySC ![]() 5w1dC ![]() 6bwnC ![]() 6bxuC ![]() 6e8fC ![]() 6eb5C ![]() 6eetC ![]() 6n22C ![]() 6n2eC ![]() 4apxS 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.: 1 / Mutation: G16D N369D Q370N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.62 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 0.1 M HEPES pH 7.7, 66% MPD, 4% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 9312 / % possible obs: 99.4 % / Redundancy: 9 % / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.119 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.15→3.2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.384 / Num. unique obs: 460 / Rpim(I) all: 0.616 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4APX, 5ULY Resolution: 3.15→49.99 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.869 / SU B: 44.508 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.744 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.15→49.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|