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Yorodumi- PDB-8bd9: Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 10 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bd9 | ||||||
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Title | Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 10 | ||||||
Components | E3 ubiquitin-protein ligase TRIM33 | ||||||
Keywords | TRANSCRIPTION / TRIM33 alpha / PHD-Bromo domain / complex | ||||||
Function / homology | Function and homology information co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / negative regulation of DNA-templated transcription ...co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Tassone, G. / Pozzi, C. / Palomba, T. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design. Authors: Palomba, T. / Tassone, G. / Vacca, C. / Bartalucci, M. / Valeri, A. / Pozzi, C. / Cross, S. / Siragusa, L. / Desantis, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bd9.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bd9.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/8bd9 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/8bd9 | HTTPS FTP |
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-Related structure data
Related structure data | 8bd8C 8bdyC 3u5mS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24069.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9UPN9, RING-type E3 ubiquitin transferase | ||||||
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#2: Chemical | ChemComp-QCU / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #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: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium chloride and 20 % wt/vol PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2022 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→134.95 Å / Num. obs: 4598 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 100.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.037 / Rrim(I) all: 0.077 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 633 / CC1/2: 0.766 / Rpim(I) all: 0.294 / Rrim(I) all: 0.625 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U5M Resolution: 3.2→61.68 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.866 / SU B: 33.087 / SU ML: 0.555 / Cross valid method: THROUGHOUT / ESU R Free: 0.652 / 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: 86.868 Å2
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Refine analyze | Luzzati coordinate error obs: 0.7245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→61.68 Å
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Refine LS restraints |
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