[English] 日本語
![](img/lk-miru.gif)
- PDB-4aqe: CRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4aqe | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF DEAFNESS ASSOCIATED MUTANT MOUSE CADHERIN-23 EC1- 2S70P AND PROTOCADHERIN-15 EC1-2 FORM I | ||||||
![]() |
| ||||||
![]() | CELL ADHESION / HEARING / DEAFNESS / CDH23 / PCDH15 / HETEROPHILIC | ||||||
Function / homology | ![]() detection of mechanical stimulus involved in equilibrioception / cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation ...detection of mechanical stimulus involved in equilibrioception / cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / 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 / non-motile cilium assembly / photoreceptor cell maintenance / catenin complex / adult walking behavior / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / visual perception / photoreceptor inner segment / locomotory behavior / morphogenesis of an epithelium / actin filament organization / sensory perception of sound / multicellular organism growth / response to calcium ion / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P. | ||||||
![]() | ![]() Title: Structure of a Force-Conveying Cadherin Bond Essential for Inner-Ear Mechanotransduction Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 198.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 157 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4apxSC ![]() 4aq8C ![]() 4aqaC ![]() 4axwC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 23866.471 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 24-228 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 27502.619 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 27-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 412 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEEREDSequence details | RESIDUE SERINE 70 (DATABASE NUMBERING) IS MUTATED TO PROLINE. NOTE SEQUENCE CONFLICT OF GENBANK NP_ ...RESIDUE SERINE 70 (DATABASE NUMBERING) IS MUTATED TO PROLINE. NOTE SEQUENCE CONFLICT OF GENBANK NP_001136218.1 AND EMBL-BANK CDS AAG53891.1 WITH Q99PJ1 (YED TO FEN) | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.99 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: 0.1 M MES, 12% PEG 4000, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→22.69 Å / Num. obs: 27207 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.27→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 96.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4APX Resolution: 2.27→22.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.058 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.N-TERMINAL METHIONINES ARE A CLONING ARTIFACT. ADDITIONAL C-TERMINAL HIS-TAGS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.144 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→22.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|