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Yorodumi- PDB-2k3y: Solution structure of EAF3 chromo barrel domain bound to histone ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k3y | |||||||||
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Title | Solution structure of EAF3 chromo barrel domain bound to histone h3 with a dimethyllysine analog H3K36ME2 | |||||||||
Components | Chromatin modification-related protein EAF3 | |||||||||
Keywords | TRANSCRIPTION REGULATOR / Eaf3 / Dimethylated histone H3K36 / Eaf3-H3K36me2 fusion / Chromo barrel domain / Histone deacetylase / Chromatin regulator / DNA damage / DNA repair / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Chromosomal protein / DNA-binding | |||||||||
Function / homology | Function and homology information nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / nucleosome assembly / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Mer, G. / Xu, C. | |||||||||
Citation | Journal: Structure / Year: 2008 Title: Structural Basis for the Recognition of Methylated Histone H3K36 by the Eaf3 Subunit of Histone Deacetylase Complex Rpd3S. Authors: Xu, C. / Cui, G. / Botuyan, M.V. / Mer, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k3y.cif.gz | 825.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k3y.ent.gz | 700.2 KB | Display | PDB format |
PDBx/mmJSON format | 2k3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/2k3y ftp://data.pdbj.org/pub/pdb/validation_reports/k3/2k3y | 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: 15367.364 Da / Num. of mol.: 1 / Fragment: UNP residues 1 to 115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: EAF3, YPR023C, YP9367.03C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12432 |
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Nonpolymer details | HIS RESIDUES HAVE HYDROGENS ONLY ON THE EPSILON NITROGEN |
-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 | Ionic strength: 50 / pH: 6.7 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / 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 |