+Open data
-Basic information
Entry | Database: PDB / ID: 5h1t | ||||||
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Title | Complex structure of TRIM24 PHD-bromodomain and inhibitor 1 | ||||||
Components | Transcription intermediary factor 1-alpha | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION INHIBITOR / TRANSCRIPTION / TRANSCRIPTION INHIBITOR / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex | ||||||
Function / homology | Function and homology information perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / male germ cell nucleus / calcium ion homeostasis / epithelial cell proliferation / lysine-acetylated histone binding / Signaling by FGFR1 in disease ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / male germ cell nucleus / calcium ion homeostasis / epithelial cell proliferation / lysine-acetylated histone binding / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / nuclear receptor binding / RING-type E3 ubiquitin transferase / regulation of protein stability / euchromatin / protein catabolic process / p53 binding / response to peptide hormone / negative regulation of epithelial cell proliferation / ubiquitin protein ligase activity / Signaling by BRAF and RAF1 fusions / regulation of apoptotic process / transcription coactivator activity / transcription by RNA polymerase II / protein kinase activity / protein ubiquitination / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / chromatin / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å | ||||||
Authors | Liu, J. | ||||||
Citation | Journal: FEBS J. / Year: 2017 Title: The polar warhead of a TRIM24 bromodomain inhibitor rearranges a water-mediated interaction network Authors: Liu, J. / Li, F. / Bao, H. / Jiang, Y. / Zhang, S. / Ma, R. / Gao, J. / Wu, J. / Ruan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h1t.cif.gz | 303.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1t.ent.gz | 245.4 KB | Display | PDB format |
PDBx/mmJSON format | 5h1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h1t_validation.pdf.gz | 482.4 KB | Display | wwPDB validaton report |
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Full document | 5h1t_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 5h1t_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 5h1t_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1t ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1t | HTTPS FTP |
-Related structure data
Related structure data | 5h1uC 5h1vC 3o33S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21231.316 Da / Num. of mol.: 4 / Fragment: UNP residues 824-1006 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): 'BL21-Gold(DE3)pLysS AG' References: UniProt: O15164, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-7FF / #4: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium, 2%(v/v) Polyethylene glycol 400, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→40 Å / Num. obs: 52566 / % possible obs: 92.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.98 Å2 / Rmerge(I) obs: 0.089 / Net I/av σ(I): 15.147 / Net I/σ(I): 5.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O33 Resolution: 1.951→31.399 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 22.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.55 Å2 / Biso mean: 36.6442 Å2 / Biso min: 14.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.951→31.399 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Origin x: 0.6662 Å / Origin y: -0.2955 Å / Origin z: 0.1867 Å
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Refinement TLS group |
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