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Yorodumi- PDB-5yj0: Mouse Cereblon thalidomide binding domain complexed with S-form t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yj0 | ||||||
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Title | Mouse Cereblon thalidomide binding domain complexed with S-form thalidomide | ||||||
Components | Protein cereblon | ||||||
Keywords | METAL BINDING PROTEIN / Zinc binding protein | ||||||
Function / homology | Function and homology information negative regulation of large conductance calcium-activated potassium channel activity / negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination ...negative regulation of large conductance calcium-activated potassium channel activity / negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mori, T. / Hakoshima, T. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structural basis of thalidomide enantiomer binding to cereblon Authors: Mori, T. / Ito, T. / Liu, S. / Ando, H. / Sakamoto, S. / Yamaguchi, Y. / Tokunaga, E. / Shibata, N. / Handa, H. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yj0.cif.gz | 339.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yj0.ent.gz | 276.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yj0_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 5yj0_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 5yj0_validation.xml.gz | 73.9 KB | Display | |
Data in CIF | 5yj0_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/5yj0 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/5yj0 | HTTPS FTP |
-Related structure data
Related structure data | 5yizC 5yj1C 3wx2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12335.271 Da / Num. of mol.: 16 / Fragment: UNP residues 322-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crbn / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C7D2 #2: Chemical | ChemComp-EF2 / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: 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: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.0M ammonium sulfate 0.1M sodium acetate (pH5.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.28268 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28268 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 173436 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.5 / Num. unique obs: 17239 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WX2 Resolution: 1.8→38.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.751 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→38.15 Å
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