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Yorodumi- PDB-6mio: Crystal structure of Taf14 YEATS domain in complex with histone H3K9pr -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mio | ||||||
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Title | Crystal structure of Taf14 YEATS domain in complex with histone H3K9pr | ||||||
Components |
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Keywords | TRANSCRIPTION / Epigenetic / Histone reader | ||||||
Function / homology | Function and homology information 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 / telomere organization ...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 / telomere organization / Chromatin modifying enzymes / RNA polymerase II preinitiation complex assembly / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription initiation at RNA polymerase II promoter / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / 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 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / histone binding / 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 transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Klein, B.J. / Andrews, F.H. / Vann, K.R. / Kutateladze, T.G. | ||||||
Citation | Journal: Nat Commun / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mio.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mio.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mio_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 6mio_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | 6mio_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6mio_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/6mio ftp://data.pdbj.org/pub/pdb/validation_reports/mi/6mio | HTTPS FTP |
-Related structure data
Related structure data | 6milC 6mimC 6minC 6mipC 6miqC 5iokS 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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1 |
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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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189 |
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#2: Protein/peptide | Mass: 873.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 46% 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→37.06 Å / Num. obs: 16550 / % possible obs: 97.8 % / Redundancy: 4.3 % / Rsym value: 0.054 / Net I/σ(I): 51.8 |
Reflection shell | Resolution: 2→2.03 Å / Rsym value: 0.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IOK Resolution: 1.85→37.057 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→37.057 Å
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Refine LS restraints |
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LS refinement shell |
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