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- PDB-6fgn: Solution Structure of p300Taz2-p63TA -

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Basic information

Entry
Database: PDB / ID: 6fgn
TitleSolution Structure of p300Taz2-p63TA
ComponentsHistone acetyltransferase p300,Tumor protein 63
KeywordsANTITUMOR PROTEIN / p300 / CREB Binding protein / p53 family / p63 / p73
Function / homology
Function and homology information


ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / behavioral defense response ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / negative regulation of keratinocyte differentiation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / polarized epithelial cell differentiation / NOTCH2 intracellular domain regulates transcription / negative regulation of intracellular estrogen receptor signaling pathway / peptidyl-lysine acetylation / proximal/distal pattern formation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / positive regulation of fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / WW domain binding / skin morphogenesis / cranial skeletal system development / cellular response to L-leucine / histone H4 acetyltransferase activity / sympathetic nervous system development / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / post-anal tail morphogenesis / 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 / acetylation-dependent protein binding / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / 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 / regulation of androgen receptor signaling pathway / positive regulation by host of viral transcription / embryonic forelimb morphogenesis / regulation of mitochondrion organization / embryonic hindlimb morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / face morphogenesis / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / megakaryocyte development / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / macrophage derived foam cell differentiation / nuclear androgen receptor binding / regulation of tubulin deacetylation / STAT family protein binding / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / internal protein amino acid acetylation / acyltransferase activity / positive regulation of Notch signaling pathway / protein acetylation / regulation of epidermal cell division / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of transforming growth factor beta receptor signaling pathway / fat cell differentiation / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation
Similarity search - Function
Tumour protein p63, SAM 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 ...Tumour protein p63, SAM 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. / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / 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. / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Nuclear receptor coactivator, interlocking / Sterile alpha motif/pointed domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone acetyltransferase p300 / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGebel, J. / Kazemi, S. / Lohr, F. / Guntert, P. / Dotsch, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDO 545/13 1 Germany
CitationJournal: Structure / Year: 2018
Title: Regulation of the Activity in the p53 Family Depends on the Organization of the Transactivation Domain.
Authors: Krauskopf, K. / Gebel, J. / Kazemi, S. / Tuppi, M. / Lohr, F. / Schafer, B. / Koch, J. / Guntert, P. / Dotsch, V. / Kehrloesser, S.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: Histone acetyltransferase p300,Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0304
Polymers13,8341
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area9500 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone acetyltransferase p300,Tumor protein 63 / p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone ...p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone crotonyltransferase p300 / Protein propionyltransferase p300 / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p40 / p51


Mass: 13834.022 Da / Num. of mol.: 1 / Fragment: Taz2,transactivation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300, TP63, KET, P63, P73H, P73L, TP73L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q09472, UniProt: Q9H3D4, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: 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-IDSample stateSpectrometer-IDType
111isotropic43D 1H-13C NOESY aliphatic
121isotropic23D 1H-13C NOESY aromatic
131isotropic43D 1H-15N NOESY
141isotropic22D 1H-13C HSQC aromatic
151isotropic42D 1H-13C HSQC aliphatic
161isotropic12D 1H-15N HSQC
171isotropic13D HN(CA)CB
181isotropic13D HN(COCA)CB
191isotropic23D HNCO
1101isotropic23D H(CCO)NH TOCSY
1111isotropic23D C(CO)NH TOCSY

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Sample preparation

DetailsType: solution
Contents: 1200 mM [U-13C; U-15N] Fusion construct of p300 Taz2 and the transactivation domain of p63, 25 mM MES, 200 mM NaCl, 0.5 mM TCEP, 95% H2O/5% D2O
Label: 13C15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1200 mMFusion construct of p300 Taz2 and the transactivation domain of p63[U-13C; U-15N]1
25 mMMESnatural abundance1
200 mMNaClnatural abundance1
0.5 mMTCEPnatural abundance1
Sample conditionsIonic strength: 200 mM / Label: condition_1 / pH: 6.3 / Pressure: AMBIENT mbar / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE III HDBrukerAVANCE III HD7002
Bruker AVANCE III HDBrukerAVANCE III HD8003
Bruker AVANCEBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.13T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Franciscochemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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