+Open data
-Basic information
Entry | Database: PDB / ID: 2rny | |||||||||
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Title | Complex Structures of CBP Bromodomain with H4 ack20 Peptide | |||||||||
Components |
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Keywords | TRANSFERASE/NUCLEAR PROTEIN / Bromodomain / Histone / CREB / CBP / p53 / Acetylation / Activator / Chromosomal rearrangement / Disease mutation / Host-virus interaction / Metal-binding / Methylation / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Transferase / Zinc / Zinc-finger / Chromosomal protein / DNA-binding / Nucleosome core / TRANSFERASE-NUCLEAR PROTEIN COMPLEX | |||||||||
Function / homology | Function and homology information peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / embryonic digit morphogenesis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / Attenuation phase / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / cellular response to nutrient levels / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / canonical NF-kappaB signal transduction / hepoxilin biosynthetic process / regulation of cellular response to heat / histone acetyltransferase activity / linoleic acid metabolic process / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / PPARA activates gene expression / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / chromatin DNA binding / p53 binding / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of protein localization to nucleus / rhythmic process / transcription corepressor activity / cellular response to UV / Circadian Clock / HATs acetylate histones / TRAF3-dependent IRF activation pathway / DNA-binding transcription factor binding / transcription regulator complex / protein-containing complex assembly / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / response to hypoxia / nuclear body / chromatin binding / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
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 | 2rny.cif.gz | 890.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rny.ent.gz | 737.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rny_validation.pdf.gz | 357.8 KB | Display | wwPDB validaton report |
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Full document | 2rny_full_validation.pdf.gz | 597.7 KB | Display | |
Data in XML | 2rny_validation.xml.gz | 92.2 KB | Display | |
Data in CIF | 2rny_validation.cif.gz | 116.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/2rny ftp://data.pdbj.org/pub/pdb/validation_reports/rn/2rny | 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: 14418.547 Da / Num. of mol.: 1 / Fragment: UNP residues 1081-1197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): BL21 / References: UniProt: Q92793, histone acetyltransferase |
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#2: Protein/peptide | Mass: 1795.079 Da / Num. of mol.: 1 / Fragment: UNP residues 14-28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): BL21 / References: UniProt: P62805 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 1H-13C NOESY |
-Sample preparation
Details | Contents: 0.5mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O Solvent system: 100% D2O |
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Sample | Conc.: 0.5 mM / Component: sodium phosphate / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.1 / 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 |