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Yorodumi- PDB-5crv: Crystal structure of the Bro domain of HD-PTP in a complex with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5crv | ||||||
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Title | Crystal structure of the Bro domain of HD-PTP in a complex with the core region of STAM2 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / HD-PTP / Bro domain / STAM2 / ESCRT-0 / EGFR | ||||||
Function / homology | Function and homology information positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / ESCRT-0 complex / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of homophilic cell adhesion / positive regulation of adherens junction organization / ESCRT-0 complex / positive regulation of Wnt protein secretion / positive regulation of early endosome to late endosome transport / negative regulation of epithelial cell migration / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endocytic recycling / Interleukin-37 signaling / RHOU GTPase cycle / endocytic vesicle / cilium assembly / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / protein-tyrosine-phosphatase / EGFR downregulation / InlB-mediated entry of Listeria monocytogenes into host cell / ciliary basal body / ubiquitin binding / protein tyrosine phosphatase activity / macroautophagy / Negative regulation of MET activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / endosome / early endosome / nuclear body / Ub-specific processing proteases / intracellular membrane-bounded organelle / protein kinase binding / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Lee, J. / Ku, B. / Kim, S.J. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Structural Study of the HD-PTP Bro1 Domain in a Complex with the Core Region of STAM2, a Subunit of ESCRT-0 Authors: Lee, J. / Oh, K.-J. / Lee, D. / Kim, B.Y. / Choi, J.S. / Ku, B. / Kim, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5crv.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5crv.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 5crv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/5crv ftp://data.pdbj.org/pub/pdb/validation_reports/cr/5crv | HTTPS FTP |
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-Related structure data
Related structure data | 5cruC 3rauS C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 40584.816 Da / Num. of mol.: 2 / Fragment: UNP residues 1-361 / Mutation: N33A,Y34A 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: 2370.781 Da / Num. of mol.: 2 / Fragment: UNP residues 350-370 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75886 #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Bis-Tris, 30%(w/v) polyethylene glycol 3350, 4%(v/v) acetonitrile |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 56289 / % possible obs: 97.3 % / Redundancy: 4.8 % / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2→2.03 Å / Mean I/σ(I) obs: 4.6 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RAU Resolution: 2.001→29.089 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 23.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→29.089 Å
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Refine LS restraints |
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LS refinement shell |
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