+Open data
-Basic information
Entry | Database: PDB / ID: 4tzc | ||||||
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Title | Crystal Structure of Murine Cereblon in Complex with Thalidomide | ||||||
Components | Protein cereblon | ||||||
Keywords | LIGASE / Ubiquitin ligase / DCAF | ||||||
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 / Resolution: 1.88 Å | ||||||
Authors | Chamberlain, P.P. / Pagarigan, B. / Delker, S. / Leon, B. | ||||||
Citation | Journal: to be published Title: Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Leon, B. / Rychak, E. / Corral, L. / Ren, Y. / Wang, M. / Riley, M. / Delker, S. / Ito, T. / Hideki, A. / ...Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Leon, B. / Rychak, E. / Corral, L. / Ren, Y. / Wang, M. / Riley, M. / Delker, S. / Ito, T. / Hideki, A. / 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 | 4tzc.cif.gz | 176.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tzc.ent.gz | 142.1 KB | Display | PDB format |
PDBx/mmJSON format | 4tzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/4tzc ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tzc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 12057.911 Da / Num. of mol.: 4 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-ZN / #3: Chemical | ChemComp-EF2 / #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: 2.55 Å3/Da / Density % sol: 51.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 100mM Sodium Acetate pH 5, 600-800mM Ammonium Sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→50 Å / Num. obs: 76864 / % possible obs: 99.9 % / Redundancy: 22.8 % / Rmerge(I) obs: 0.089 / Χ2: 1.019 / Net I/av σ(I): 38.415 / Net I/σ(I): 9.7 / Num. measured all: 1750335 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.102 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 29.609 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.88→50 Å
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Refine LS restraints |
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