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- PDB-3u5o: Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u5o | ||||||
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Title | Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide | ||||||
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![]() | TRANSCRIPTION / TRIM33 / PHD / Bromodomain / TGF-beta / epigenetics / histone / methylation / K9me3 / K14ac / K18ac | ||||||
Function / homology | ![]() 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / 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 / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z. / Patel, D.J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 660.9 KB | Display | ![]() |
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PDB format | ![]() | 554.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 594.8 KB | Display | ![]() |
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Full document | ![]() | 656 KB | Display | |
Data in XML | ![]() | 64.3 KB | Display | |
Data in CIF | ![]() | 85.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3u5mC ![]() 3u5nC ![]() 3u5pC ![]() 3o33S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23830.262 Da / Num. of mol.: 8 / Fragment: The PHD and Bromo domain of TRIM33 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UPN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | Mass: 2486.892 Da / Num. of mol.: 8 Fragment: N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23 Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) ![]() #3: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 197 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Monochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 52739 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 54.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 5307 / Rsym value: 0.582 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3O33 Resolution: 2.7→28.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 35.428 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 96.953 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→28.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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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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