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- PDB-2kje: NMR structure of CBP TAZ2 and adenoviral E1A complex -

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Basic information

Entry
Database: PDB / ID: 2kje
TitleNMR structure of CBP TAZ2 and adenoviral E1A complex
Components
  • CREB-binding protein
  • Early E1A 32 kDa protein
KeywordsTRANSCRIPTION / CBP / TAZ2 / E1A / adenoviral / Acetylation / Activator / Bromodomain / Chromosomal rearrangement / Disease mutation / Host-virus interaction / Isopeptide bond / Metal-binding / Methylation / Nucleus / Phosphoprotein / Transcription regulation / Transferase / Ubl conjugation / Zinc / Zinc-finger / Alternative splicing / DNA-binding / Early protein / Oncogene
Function / homology
Function and homology information


regulation by virus of viral protein levels in host cell / molecular sequestering activity / positive regulation of protein sumoylation / 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 / histone H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity ...regulation by virus of viral protein levels in host cell / molecular sequestering activity / positive regulation of protein sumoylation / 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 / histone H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / MRF binding / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / negative regulation of transcription by RNA polymerase I / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / homeostatic process / Notch-HLH transcription pathway / protein acetylation / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / Attenuation phase / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / regulation of cellular response to heat / histone acetyltransferase activity / 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 / protein destabilization / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / regulation of protein localization / Circadian Clock / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / response to hypoxia / molecular adaptor activity / nuclear body / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription
Similarity search - Function
Adenovirus early E1A protein / Early E1A protein / CREB-binding Protein; Chain A / TAZ 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 ...Adenovirus early E1A protein / Early E1A protein / CREB-binding Protein; Chain A / TAZ 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. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Early E1A protein / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus 5
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsFerreon, J.C. / Martinez-Yamout, M. / Dyson, H. / Wright, P.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for subversion of cellular control mechanisms by the adenoviral E1A oncoprotein.
Authors: Ferreon, J.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CREB-binding protein
B: Early E1A 32 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1895
Polymers14,9922
Non-polymers1963
Water0
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: 10527.567 Da / Num. of mol.: 1 / Fragment: UNP residues 1763-1854
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Protein/peptide Early E1A 32 kDa protein


Mass: 4464.908 Da / Num. of mol.: 1 / Fragment: UNP residues 53-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: P03255
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA

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Sample preparation

DetailsContents: 1-1.5 mM [U-100% 13C; U-100% 15N] TRIS-1, 1-1.5 mM [U-100% 15N] TRIS-2, 100% D2O
Solvent system: 100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTRIS-1[U-100% 13C; U-100% 15N]1-1.51
mMTRIS-2[U-100% 15N]1-1.51
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmdata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: molecular 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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