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Yorodumi- PDB-2rnw: The Structural Basis for Site-Specific Lysine-Acetylated Histone ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rnw | |||||||||
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Title | The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the Human Transcriptional Co-Activators PCAf and CBP | |||||||||
Components |
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Keywords | TRANSFERASE/NUCLEAR PROTEIN / bromodomain / histone / acetyltransferase / Acyltransferase / Cell cycle / Host-virus interaction / Nucleus / Polymorphism / Transcription / Transcription regulation / Acetylation / Chromosomal protein / DNA damage / DNA repair / DNA-binding / Methylation / Nucleosome core / Phosphoprotein / TRANSFERASE-NUCLEAR PROTEIN COMPLEX | |||||||||
Function / homology | Function and homology information sexual sporulation resulting in formation of a cellular spore / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / cupric reductase (NADH) activity / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / positive regulation of transcription from RNA polymerase II promoter by glucose / diamine N-acetyltransferase activity ...sexual sporulation resulting in formation of a cellular spore / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / cupric reductase (NADH) activity / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / positive regulation of transcription from RNA polymerase II promoter by glucose / diamine N-acetyltransferase activity / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Condensation of Prophase Chromosomes / Physiological factors / SIRT1 negatively regulates rRNA expression / peptidyl-lysine acetylation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / Assembly of the ORC complex at the origin of replication / YAP1- and WWTR1 (TAZ)-stimulated gene expression / positive regulation of fatty acid biosynthetic process / actomyosin / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / replication fork protection complex / N-terminal peptidyl-lysine acetylation / Oxidative Stress Induced Senescence / ATAC complex / I band / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / limb development / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / A band / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / histone acetyltransferase binding / protein acetylation / positive regulation of transcription by RNA polymerase I / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / RNA Polymerase I Promoter Escape / regulation of cell division / nucleolar large rRNA transcription by RNA polymerase I / acetyltransferase activity / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / Estrogen-dependent gene expression / rRNA transcription / regulation of embryonic development / CENP-A containing nucleosome / intracellular copper ion homeostasis / regulation of DNA repair / histone acetyltransferase activity / histone acetyltransferase / transcription coregulator activity / positive regulation of gluconeogenesis / positive regulation of glycolytic process / transcription initiation-coupled chromatin remodeling / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / vasodilation / cellular response to insulin stimulus / aerobic respiration / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / kinetochore / memory / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of neuron projection development / structural constituent of chromatin / rhythmic process / nucleosome / chromatin organization / heart development / HATs acetylate histones / cellular response to oxidative stress / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / chromatin remodeling / regulation of cell cycle / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin binding / centrosome / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | |||||||||
Authors | Zeng, L. / Zhang, Q. / Gerona-Navarro, G. / Zhou, M.M. | |||||||||
Citation | Journal: Structure / Year: 2008 Title: Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300 Authors: Zeng, L. / Zhang, Q. / Gerona-Navarro, G. / Moshkina, N. / 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 | 2rnw.cif.gz | 852.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rnw.ent.gz | 713.6 KB | Display | PDB format |
PDBx/mmJSON format | 2rnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rnw_validation.pdf.gz | 367.9 KB | Display | wwPDB validaton report |
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Full document | 2rnw_full_validation.pdf.gz | 624.3 KB | Display | |
Data in XML | 2rnw_validation.xml.gz | 92.8 KB | Display | |
Data in CIF | 2rnw_validation.cif.gz | 119.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/2rnw ftp://data.pdbj.org/pub/pdb/validation_reports/rn/2rnw | HTTPS FTP |
-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: 14052.226 Da / Num. of mol.: 1 / Fragment: UNP residues 719-832 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q92831, histone acetyltransferase |
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#2: Protein/peptide | Mass: 1606.826 Da / Num. of mol.: 1 / Fragment: UNP residues 2-16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P61830 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-100% 13C; U-100% 15N] potassium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: potassium phosphate / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 |