+Open data
-Basic information
Entry | Database: PDB / ID: 7bqu | ||||||
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Title | Cereblon in complex with SALL4 and (S)-thalidomide | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / ZINC FINGER / E3 UBIQUITIN LIGASE / COMPLEX / THALIDOMIDE | ||||||
Function / homology | Function and homology information POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of monoatomic ion transmembrane transport / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / Cul4A-RING E3 ubiquitin ligase complex / inner cell mass cell proliferation / ventricular septum development / locomotory exploration behavior / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of monoatomic ion transmembrane transport / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / Cul4A-RING E3 ubiquitin ligase complex / inner cell mass cell proliferation / ventricular septum development / locomotory exploration behavior / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / Potential therapeutics for SARS / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Furihata, H. / Miyauchi, Y. / Asano, A. / Tanokura, M. / Miyakawa, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide. Authors: Furihata, H. / Yamanaka, S. / Honda, T. / Miyauchi, Y. / Asano, A. / Shibata, N. / Tanokura, M. / Sawasaki, T. / Miyakawa, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bqu.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bqu.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 7bqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/7bqu ftp://data.pdbj.org/pub/pdb/validation_reports/bq/7bqu | HTTPS FTP |
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-Related structure data
Related structure data | 7bqvC 4tz4S 5yj0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12614.542 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2 | ||||
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#2: Protein/peptide | Mass: 3130.653 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4, ZNF797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4 | ||||
#3: Chemical | ChemComp-EF2 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.99 Å / Num. obs: 11808 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.044 / Rrim(I) all: 0.158 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 746 / CC1/2: 0.826 / Rpim(I) all: 0.363 / Rrim(I) all: 1.31 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TZ4, 5YJ0 Resolution: 1.9→34.674 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→34.674 Å
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Refine LS restraints |
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LS refinement shell |
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