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Yorodumi- PDB-1uj0: Crystal Structure of STAM2 SH3 domain in complex with a UBPY-deri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uj0 | ||||||
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Title | Crystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN/SIGNALING PROTEIN / STAM / SH3 / deubiquitinating enzyme / Grb2 / Gads / PXXP / Hrs / endocytosis / early endosome / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information extrinsic component of endosome membrane / Downregulation of ERBB2:ERBB3 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of MET activity / Regulation of FZD by ubiquitination / EGFR downregulation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Cargo recognition for clathrin-mediated endocytosis / protein K48-linked deubiquitination / endosome organization ...extrinsic component of endosome membrane / Downregulation of ERBB2:ERBB3 signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of MET activity / Regulation of FZD by ubiquitination / EGFR downregulation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Cargo recognition for clathrin-mediated endocytosis / protein K48-linked deubiquitination / endosome organization / Clathrin-mediated endocytosis / Ub-specific processing proteases / protein K63-linked deubiquitination / extrinsic component of plasma membrane / protein deubiquitination / mitotic cytokinesis / endocytic vesicle / cellular response to nerve growth factor stimulus / intracellular protein transport / regulation of protein stability / SH3 domain binding / regulation of protein localization / positive regulation of canonical Wnt signaling pathway / early endosome membrane / midbody / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ras protein signal transduction / dendritic spine / postsynaptic density / early endosome / intracellular membrane-bounded organelle / glutamatergic synapse / signal transduction / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kaneko, T. / Kumasaka, T. / Ganbe, T. / Sato, T. / Miyazawa, K. / Kitamura, N. / Tanaka, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain. Authors: Kaneko, T. / Kumasaka, T. / Ganbe, T. / Sato, T. / Miyazawa, K. / Kitamura, N. / Tanaka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uj0.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uj0.ent.gz | 18.1 KB | Display | PDB format |
PDBx/mmJSON format | 1uj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uj0_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 1uj0_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 1uj0_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1uj0_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/1uj0 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/1uj0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 7059.673 Da / Num. of mol.: 1 / Fragment: RESIDUES 200-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: O88811 |
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#2: Protein/peptide | Mass: 1284.483 Da / Num. of mol.: 1 / Fragment: RESIDUES 699-709 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: GenBank: 11414862, UniProt: Q80U87*PLUS |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.97 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.08M Sodium Phosphate monobasic, 1.92M Potassium phosphate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 2, 2002 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.1 Å / Num. obs: 8501 / % possible obs: 97.9 % / Observed criterion σ(I): 6 |
Reflection shell | Resolution: 1.7→1.79 Å / % possible all: 96.8 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.11 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.525 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.802 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20 /
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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