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- PDB-5crv: Crystal structure of the Bro domain of HD-PTP in a complex with t... -
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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 | ||||||
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![]() | PROTEIN TRANSPORT / HD-PTP / Bro domain / STAM2 / ESCRT-0 / EGFR | ||||||
Function / homology | ![]() 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 / dephosphorylation / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / protein-tyrosine-phosphatase / InlB-mediated entry of Listeria monocytogenes into host cell / ciliary basal body / ubiquitin binding / protein tyrosine phosphatase activity / macroautophagy / EGFR downregulation / Negative regulation of MET activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / early endosome / nuclear body / Ub-specific processing proteases / endosome / intracellular membrane-bounded organelle / protein kinase binding / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, J. / Ku, B. / Kim, S.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.4 KB | Display | ![]() |
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PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.3 KB | Display | ![]() |
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Full document | ![]() | 466.4 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cruC ![]() 3rauS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2370.781 Da / Num. of mol.: 2 / Fragment: UNP residues 350-370 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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