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- PDB-2k8f: Structural Basis for the Regulation of p53 Function by p300 -

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Basic information

Entry
Database: PDB / ID: 2k8f
TitleStructural Basis for the Regulation of p53 Function by p300
Components
  • Cellular tumor antigen p53
  • Histone acetyltransferase p300
KeywordsTransferase/Transcription / Complex of p53 and p300 / Acetylation / Bromodomain / Cell cycle / Chromosomal rearrangement / Citrullination / Disease mutation / Host-virus interaction / Metal-binding / Methylation / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / Transferase / Zinc / Zinc-finger / Activator / Alternative splicing / Anti-oncogene / Apoptosis / Covalent protein-RNA linkage / Cytoplasm / DNA-binding / Endoplasmic reticulum / Glycoprotein / Li-Fraumeni syndrome / Ubl conjugation / Transferase-Transcription COMPLEX
Function / homology
Function and homology information


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 ...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 / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / cellular response to L-leucine / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / histone H3K18 acetyltransferase activity / STAT3 nuclear events downstream of ALK signaling / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / TGFBR3 expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / positive regulation by host of viral transcription / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / circadian behavior / bone marrow development / face morphogenesis / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / germ cell nucleus / histone deacetylase regulator activity / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / regulation of glycolytic process / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Regulation of NFE2L2 gene expression / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / NOTCH3 Intracellular Domain Regulates Transcription / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / platelet formation / TRAF6 mediated IRF7 activation / negative regulation of glial cell proliferation / FOXO-mediated transcription of cell death genes / peptide-lysine-N-acetyltransferase activity / megakaryocyte development / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / macrophage derived foam cell differentiation / regulation of tubulin deacetylation / nuclear androgen receptor binding / mitochondrial DNA repair / T cell lineage commitment / STAT family protein binding
Similarity search - Function
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 ...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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / 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 / p53-like transcription factor, DNA-binding / 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
Cellular tumor antigen p53 / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsBai, Y. / Feng, H. / Jenkins, L.M. / Durell, S.R. / Wiodawer, A. / Appella, E.
CitationJournal: Structure / Year: 2009
Title: Structural Basis for p300 Taz2-p53 TAD1 Binding and Modulation by Phosphorylation.
Authors: Feng, H. / Jenkins, L.M. / Durell, S.R. / Hayashi, R. / Mazur, S.J. / Cherry, S. / Tropea, J.E. / Miller, M. / Wlodawer, A. / Appella, E. / Bai, Y.
History
DepositionSep 8, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase p300
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)14,3162
Polymers14,3162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Histone acetyltransferase p300 / E1A-associated protein p300


Mass: 9963.786 Da / Num. of mol.: 1 / Fragment: UNP residues 1723-1812 / Mutation: C1738A, C1746A, C1789A, C1790A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus (DE3)-RIL / References: UniProt: Q09472, histone acetyltransferase
#2: Protein/peptide Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 4351.771 Da / Num. of mol.: 1 / Fragment: UNP residues 1-39
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / Strain (production host): Topp2 / References: UniProt: P04637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The structure of p53(1-39) and p300 complex was determined by NMR.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1242D 1H-1H NOESY
1333D CBCA(CO)NH
1433D HN(CA)CB
1533D HNCO
1633D HN(CA)CO
1733D HNCA
1833D H(CCO)NH
1933D (H)CCH-TOCSY
11023D HNHA
11123D 1H-15N NOESY
11233D 1H-13C NOESY
11312D 1H-15N HSQC
11413D CBCA(CO)NH
11513D HN(CA)CB
11613D HNCA
11713D HNCO
11813D HN(CA)CO
11913D H(CCO)NH
12013D (H)CCH-TOCSY
12113D 1H-15N NOESY
12213D 1H-13C NOESY
NMR detailsText: All the data related to chemical shift assignments were collected by 500 MHz, and 3D NOESY data were recorded by 700 MHz.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM TAZ2, 1.0 mM [U-100% 15N] TAD(1-39), 1.0 mM [U-100% 13C; U-100% 15N] TAD(1-39), 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 15N] TAZ2, 1.1 mM TAD(1-39), 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] TAZ2, 1.1 mM TAD(1-39), 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM TAZ2, 1.1 mM TAD(1-39), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMTAD(1-39)[U-100% 15N]1
1.0 mMTAD(1-39)[U-100% 13C; U-100% 15N]4
1.0 mMTAZ2[U-100% 15N]2
1.0 mMTAZ2[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 200 / pH: 6.3 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameVersionDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeupdatedDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewupdatedJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOSupdatedCornilescu, Delaglio and Baxstructure solution
ProcheckNMRupdatedLaskowski and MacArthurstructure validation
MolProbity3.15Richardsonstructure validation
Insight IIupdatedAccelrys Software Inc.figure preparation
SYBYL8Triposstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 1732 / NOE intraresidue total count: 521 / NOE long range total count: 253 / NOE medium range total count: 473 / NOE sequential total count: 499 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 114
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 3.58 ° / Maximum upper distance constraint violation: 0.33 Å
NMR ensemble rmsDistance rms dev: 0.05 Å / Distance rms dev error: 0.003 Å

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