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Yorodumi- PDB-3wx1: Mouse Cereblon thalidomide binding domain, selenomethionine derivative -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wx1 | ||||||
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Title | Mouse Cereblon thalidomide binding domain, selenomethionine derivative | ||||||
Components | Protein cereblon | ||||||
Keywords | METAL BINDING PROTEIN / Zinc Finger / E3 ubiquitin ligase | ||||||
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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å | ||||||
Authors | Mori, T. / Ito, T. / Hirano, Y. / Yamaguchi, Y. / Handa, H. / Hakoshima, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Chie-Leon, B. / Rychak, E. / Corral, L.G. / Ren, Y.J. / Wang, M. / Riley, M. / Delker, S.L. / Ito, T. / Ando, ...Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Chie-Leon, B. / Rychak, E. / Corral, L.G. / Ren, Y.J. / Wang, M. / Riley, M. / Delker, S.L. / Ito, T. / Ando, H. / Mori, T. / Hirano, Y. / Handa, H. / Hakoshima, T. / Daniel, T.O. / Cathers, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wx1.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wx1.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/3wx1 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/3wx1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12429.062 Da / Num. of mol.: 2 / Fragment: Cereblon(CRBN), UNP residues 322-427 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 | #3: Chemical | ChemComp-SO4 / #4: 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: 2.76 Å3/Da / Density % sol: 55.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.7 Details: 0.1M sodium acetate (pH 5.7), 0.2M sodium sulphate, 12% PEG3350, 30% glycerol, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97911, 0.99513, 0.97941 | ||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 26, 2011 | ||||||||||||
Radiation | Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.93→50 Å / Num. all: 20774 / Num. obs: 20774 / % possible obs: 100 % |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 1.93→34.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.183 / SU ML: 0.092 / ESU R: 0.139 / ESU R Free: 0.125 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→34.1 Å
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Refine LS restraints |
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