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Yorodumi- PDB-6i7a: Co-crystal structure of human SPOP MATH domain (D140N) and human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i7a | ||||||
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Title | Co-crystal structure of human SPOP MATH domain (D140N) and human BRD3 fragment | ||||||
Components |
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Keywords | LIGASE / ligase nuclear cancer ubiquitination | ||||||
Function / homology | Function and homology information regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / localization / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding ...regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / localization / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding / protein polyubiquitination / chromatin organization / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ostertag, M.S. / Popowicz, G.M. / Sattler, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Structural Insights into BET Client Recognition of Endometrial and Prostate Cancer-Associated SPOP Mutants. Authors: Ostertag, M.S. / Hutwelker, W. / Plettenburg, O. / Sattler, M. / Popowicz, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i7a.cif.gz | 245.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i7a.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 6i7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/6i7a ftp://data.pdbj.org/pub/pdb/validation_reports/i7/6i7a | HTTPS FTP |
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-Related structure data
Related structure data | 6i41SC 6i5pC 6i68C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16615.152 Da / Num. of mol.: 4 / Mutation: D140N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43791 #2: Protein/peptide | Mass: 935.995 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15059 #3: 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: 2.49 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→8.72 Å / Num. obs: 51096 / % possible obs: 99.9 % / Redundancy: 8.48 % / CC1/2: 0.999 / Net I/σ(I): 14.71 |
Reflection shell | Resolution: 1.95→1.999 Å / Num. unique obs: 3725 / CC1/2: 0.271 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I41 Resolution: 2.2→19.912 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.912 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.9389 Å / Origin y: 13.1948 Å / Origin z: -0.6617 Å
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Refinement TLS group | Selection details: all |