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Yorodumi- PDB-1wum: Complex structure of PCAF bromodomain with small chemical ligand NP2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wum | ||||||
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Title | Complex structure of PCAF bromodomain with small chemical ligand NP2 | ||||||
Components | Histone acetyltransferase PCAF | ||||||
Keywords | TRANSFERASE / BROMODOMAIN / HISTONE-ACETYLTRANSFERASE / NMR-STRUCTURE / CHEMICAL LIGAND / NP2 / NP1 | ||||||
Function / homology | Function and homology information regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / peptidyl-lysine acetylation ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / 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 / N-terminal peptidyl-lysine acetylation / ATAC complex / I band / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / SAGA complex / limb development / A band / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of tubulin deacetylation / peptide-lysine-N-acetyltransferase activity / histone acetyltransferase binding / protein acetylation / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / Formation of paraxial mesoderm / acetyltransferase activity / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / 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 / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / mitotic spindle / memory / kinetochore / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of neuron projection development / histone deacetylase binding / cellular response to insulin stimulus / vasodilation / rhythmic process / cellular response to oxidative stress / heart development / HATs acetylate histones / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Authors | Zeng, L. / Li, J. / Muller, M. / Yan, S. / Mujtaba, S. / Pan, C. / Wang, Z. / Zhou, M.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Selective small molecules blocking HIV-1 Tat and coactivator PCAF association Authors: Zeng, L. / Li, J. / Muller, M. / Yan, S. / Mujtaba, S. / Pan, C. / Wang, Z. / 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 | 1wum.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wum.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/1wum ftp://data.pdbj.org/pub/pdb/validation_reports/wu/1wum | 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: 14052.226 Da / Num. of mol.: 1 / Fragment: BROMODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92831, histone acetyltransferase |
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#2: Chemical | ChemComp-NP2 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: HNCACB, HN(CO)CACB, HCCH_TOCSY, (H)C(CO)NH_TOCSY, HNHA, 2D_1H_ROESY |
-Sample preparation
Details | Contents: 0.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT Solvent system: 10% D2O |
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Sample conditions | pH: 6.5 / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 / Details: SIMULATED ANNEALING | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 1 |