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Yorodumi- PDB-5mk1: Crystal structure of the His Domain Protein Tyrosine Phosphatase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mk1 | ||||||||||||
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Title | Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4A peptide complex structure) | ||||||||||||
Components |
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Keywords | HYDROLASE / ESCRT-III CHMP4A | ||||||||||||
Function / homology | Function and homology information positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / 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 adherens junction organization / positive regulation of homophilic cell adhesion / 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 / Sealing of the nuclear envelope (NE) by ESCRT-III / nuclear membrane reassembly / post-translational protein targeting to endoplasmic reticulum membrane / midbody abscission / multivesicular body sorting pathway / vesicle budding from membrane / early endosome to late endosome transport / membrane coat / membrane fission / plasma membrane repair / 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 / nucleus organization / Macroautophagy / mitotic metaphase chromosome alignment / viral budding via host ESCRT complex / autophagosome maturation / autophagosome membrane / cilium assembly / protein polymerization / Pyroptosis / nuclear pore / dephosphorylation / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / protein-tyrosine-phosphatase / HCMV Late Events / ciliary basal body / 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 / nuclear body / early endosome / 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Levy, C. / Gahloth, D. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Structure / Year: 2017 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mk1.cif.gz | 582.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mk1.ent.gz | 482.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/5mk1 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/5mk1 | HTTPS FTP |
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-Related structure data
Related structure data | 5mjyC 5mjzC 5mk0C 5mk2C 5mk3C 3rauS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 40719.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN23, KIAA1471 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3S7, protein-tyrosine-phosphatase #2: Protein/peptide | Mass: 2088.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BY43 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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