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- PDB-6miq: Crystal structure of Taf14 YEATS domain in complex with histone H3K9bu -
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Open data
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Basic information
Entry | Database: PDB / ID: 6miq | ||||||
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Title | Crystal structure of Taf14 YEATS domain in complex with histone H3K9bu | ||||||
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![]() | TRANSCRIPTION / Epigenetic / Histone reader | ||||||
Function / homology | ![]() NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / transcription factor TFIIF complex / Ino80 complex / mediator complex / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Chromatin modifying enzymes ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / transcription factor TFIIF complex / Ino80 complex / mediator complex / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Chromatin modifying enzymes / RNA polymerase II preinitiation complex assembly / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / 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 / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription by RNA polymerase II / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Klein, B.J. / Andrews, F.H. / Vann, K.R. / Kutateladze, T.G. | ||||||
![]() | ![]() Title: Structural insights into the pi-pi-pi stacking mechanism and DNA-binding activity of the YEATS domain. Authors: Klein, B.J. / Vann, K.R. / Andrews, F.H. / Wang, W.W. / Zhang, J. / Zhang, Y. / Beloglazkina, A.A. / Mi, W. / Li, Y. / Li, H. / Shi, X. / Kutateladze, A.G. / Strahl, B.D. / Liu, W.R. / Kutateladze, T.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.3 KB | Display | ![]() |
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PDB format | ![]() | 59.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6milC ![]() 6mimC ![]() 6minC ![]() 6mioC ![]() 6mipC ![]() 5iokS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16180.497 Da / Num. of mol.: 1 / Fragment: YEATS domain residues 1-137 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 888.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→98 Å / Num. obs: 31249 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rsym value: 0.048 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.75→1.81 Å / Rsym value: 0.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IOK Resolution: 1.75→56.575 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→56.575 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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