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Yorodumi- PDB-2ndf: Solution NMR structures of AF9 yeats domain in complex with histo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ndf | |||||||||
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Title | Solution NMR structures of AF9 yeats domain in complex with histon H3 acetylation at K18 | |||||||||
Components |
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Keywords | TRANSCRIPTION / Histone / crotonylation | |||||||||
Function / homology | Function and homology information modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / transcription elongation factor complex / 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 / negative regulation of canonical Wnt signaling pathway / lysine-acetylated histone binding / 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 / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 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 / molecular adaptor activity / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics | |||||||||
Model details | lowest energy, model1 | |||||||||
Authors | Zeng, L. / Zhou, M. | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain. Authors: Zhang, Q. / Zeng, L. / Zhao, C. / Ju, Y. / Konuma, T. / Zhou, M.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ndf.cif.gz | 983.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ndf.ent.gz | 823 KB | Display | PDB format |
PDBx/mmJSON format | 2ndf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/2ndf ftp://data.pdbj.org/pub/pdb/validation_reports/nd/2ndf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16611.160 Da / Num. of mol.: 1 / Fragment: YEATS domain residues 1-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / Strain (production host): RIL strain cells / References: UniProt: P42568 |
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#2: Protein/peptide | Mass: 1370.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P68431*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 7.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, torsion angle dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |