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Yorodumi- PDB-3u5n: Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u5n | ||||||
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Title | Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / TRIM33 / PHD / Bromodomain / TGF-beta / epigenetics / histone / methylation / K9me3 / K14ac | ||||||
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin-protein transferase activity / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein ubiquitination / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wang, Z. / Patel, D.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: A Poised Chromatin Platform for TGF-beta access to master regulators Authors: Xi, Q. / Wang, Z. / Zaromytidou, A.I. / Zhang, X.H. / Chow-Tsang, L.F. / Liu, J.X. / Kim, H. / Barlas, A. / Manova-Todorova, K. / Kaartinen, V. / Studer, L. / Mark, W. / Patel, D.J. / Massague, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u5n.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u5n.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 3u5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/3u5n ftp://data.pdbj.org/pub/pdb/validation_reports/u5/3u5n | HTTPS FTP |
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-Related structure data
Related structure data | 3u5mSC 3u5oC 3u5pC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23830.262 Da / Num. of mol.: 2 Fragment: The C-terminal PHD and Bromo dual domains of TRIM33, UNP residues 882-1087 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid details: ?469008 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9UPN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | Mass: 2273.682 Da / Num. of mol.: 2 Fragment: N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21 Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 #3: Chemical | ChemComp-ZN / #4: 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: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 197 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.28215 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2011 |
Radiation | Monochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28215 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 32561 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.091 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 32561 / Rsym value: 0.495 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U5M Resolution: 1.95→29.792 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.925 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→29.792 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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