[English] 日本語
![](img/lk-miru.gif)
- PDB-5mk1: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mk1 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) | ||||||||||||
![]() |
| ||||||||||||
![]() | HYDROLASE / ESCRT-III CHMP4A | ||||||||||||
Function / homology | ![]() positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / membrane invagination / plasma membrane tubulation / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / late endosome to lysosome transport ...positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / membrane invagination / plasma membrane tubulation / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / post-translational protein targeting to endoplasmic reticulum membrane / multivesicular body sorting pathway / membrane coat / vesicle budding from membrane / plasma membrane repair / membrane fission / early endosome to late endosome transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / endocytic recycling / nervous system process / Translation of Replicase and Assembly of the Replication Transcription Complex / Interleukin-37 signaling / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / protein polymerization / cilium assembly / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / protein-tyrosine-phosphatase / viral budding from plasma membrane / ciliary basal body / HCMV Late Events / protein tyrosine phosphatase activity / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / cytoplasmic side of plasma membrane / kinetochore / autophagy / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / ATPase binding / early endosome / nuclear body / endosome / lysosomal membrane / intracellular membrane-bounded organelle / lipid binding / protein kinase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Levy, C. / Gahloth, D. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural Basis for Specific Interaction of TGF beta Signaling Regulators SARA/Endofin with HD-PTP. Authors: Gahloth, D. / Levy, C. / Walker, L. / Wunderley, L. / Mould, A.P. / Taylor, S. / Woodman, P. / Tabernero, L. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 582.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 482.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5mjyC ![]() 5mjzC ![]() 5mk0C ![]() 5mk2C ![]() 5mk3C ![]() 3rauS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40719.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2088.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.1 M Tris pH 7.8, 5% (poly-glutamic acid low molecular weight polymer) 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.41 Å / Num. obs: 47548 / % possible obs: 93.05 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1342 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.94 / CC1/2: 0.442 / % possible all: 84.76 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3RAU Resolution: 2.5→28.41 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.67
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|