[English] 日本語
Yorodumi- PDB-6min: Crystal structure of Taf14 YEATS domain G82A mutant in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6min | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Taf14 YEATS domain G82A mutant in complex with histone H3K9cr | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / Epigenetic / Histone reader | ||||||
Function / homology | Function and homology information NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / mediator complex / transcription factor TFIIF complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Chromatin modifying enzymes ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Ino80 complex / mediator complex / transcription factor TFIIF complex / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA polymerase II preinitiation complex assembly / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / 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 / 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 / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / chromatin organization / Factors involved in megakaryocyte development and platelet production / 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 / chromatin / regulation of DNA-templated transcription / 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Klein, B.J. / Andrews, F.H. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6min.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6min.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 6min.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/6min ftp://data.pdbj.org/pub/pdb/validation_reports/mi/6min | HTTPS FTP |
---|
-Related structure data
Related structure data | 6milC 6mimC 6mioC 6mipC 6miqC 5iokS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16194.522 Da / Num. of mol.: 1 / Fragment: YEATS domain residues 1-137 / Mutation: G82A 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 |
---|---|
#2: Protein/peptide | Mass: 885.986 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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 30, 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: 1.9→37.14 Å / Num. obs: 15267 / % possible obs: 96.7 % / Redundancy: 4.3 % / Rsym value: 0.048 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.9→1.93 Å / Rsym value: 0.164 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IOK Resolution: 1.9→37.134 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.06
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.134 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|