+Open data
-Basic information
Entry | Database: PDB / ID: 5wyi | ||||||
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Title | The Yaf9 YEATS domain Recognizing H3K122suc Peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / YEATS domain / Succinylation / Transcriptional Factor | ||||||
Function / homology | Function and homology information Swr1 complex / NuA4 histone acetyltransferase complex / 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 ...Swr1 complex / NuA4 histone acetyltransferase complex / 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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, Y. / Hao, Q. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: To Be Published Title: The Yaf9 YEATS domain Recognizing H3K122suc Peptide Authors: Wang, Y. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wyi.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wyi.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/5wyi ftp://data.pdbj.org/pub/pdb/validation_reports/wy/5wyi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 18981.242 Da / Num. of mol.: 1 / Fragment: UNP residues 8-169 / Mutation: H57Y, T60K, Y76S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast) Strain: RM11-1a / Gene: SCRG_03242 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: B3LNW5 |
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#2: Protein | Mass: 18924.189 Da / Num. of mol.: 2 / Fragment: UNP residues 8-169 / Mutation: H57Y, T60K, Y76S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast) Strain: RM11-1a / Gene: SCRG_03242 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: B3LNW5 |
-Protein/peptide , 1 types, 1 molecules E
#3: Protein/peptide | Mass: 958.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS |
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-Non-polymers , 3 types, 480 molecules
#4: Chemical | ChemComp-SLL / ( |
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#5: Chemical | ChemComp-SIN / |
#6: 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: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: 0.2 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 39259 / % possible obs: 100 % / Redundancy: 5.4 % / Net I/σ(I): 13.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.529 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.529 Å
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LS refinement shell |
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