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- PDB-2rny: Complex Structures of CBP Bromodomain with H4 ack20 Peptide -

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Basic information

Entry
Database: PDB / ID: 2rny
TitleComplex Structures of CBP Bromodomain with H4 ack20 Peptide
Components
  • CREB-binding protein
  • Histone H4
KeywordsTRANSFERASE/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
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Arachidonate 15-lipoxygenase / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsZeng, L. / Zhang, Q. / Gerona-Navarro, G. / Zhou, M.M.
CitationJournal: 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
DepositionFeb 3, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)16,2142
Polymers16,2142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CREB-binding 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
#2: Protein/peptide Histone H4


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.5 mM / Component: sodium phosphate / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesdata analysis
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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