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- PDB-5hpd: Solution Structure of TAZ2-p53TAD -

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Entry
Database: PDB / ID: 5hpd
TitleSolution Structure of TAZ2-p53TAD
ComponentsCREB-binding protein,Cellular tumor antigen p53 fusion protein
KeywordsTRANSCRIPTION / intrinsically disordered protein / binding motif / transcriptional coactivator / protein-protein interaction / tumor suppressor / TRANSFERASE
Function / homology
Function and homology information


Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex ...Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / Regulation of lipid metabolism by PPARalpha / negative regulation of viral process / Cytoprotection by HMOX1 / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / outer kinetochore / negative regulation of interferon-beta production / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / MRF binding / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 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 / 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 / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / peroxisome proliferator activated receptor binding / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / face morphogenesis / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / negative regulation of transcription by RNA polymerase I / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of neuroblast proliferation / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / peptide-lysine-N-acetyltransferase activity / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / cellular response to hepatocyte growth factor stimulus / mitochondrial DNA repair / T cell lineage commitment / positive regulation of dendritic spine development / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / non-canonical NF-kappaB signal transduction / SMAD binding / behavioral response to cocaine / Zygotic genome activation (ZGA) / necroptotic process / acetyltransferase activity / rRNA transcription / cellular response to nutrient levels / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / negative regulation of telomere maintenance via telomerase
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. / Coactivator CBP, KIX domain superfamily / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / 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 / p53-like tetramerisation domain superfamily / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / 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
Similarity search - Domain/homology
Cellular tumor antigen p53 / Histone lysine acetyltransferase CREBBP
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsKrois, A.S. / Ferreon, J.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA096865 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein.
Authors: Krois, A.S. / Ferreon, J.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein,Cellular tumor antigen p53 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9074
Polymers17,7111
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10240 Å2
MethodPISA
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,Cellular tumor antigen p53 fusion protein / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 17711.236 Da / Num. of mol.: 1 / Fragment: p53TAD, TAZ2 domain of CBP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Crebbp, Cbp, TP53, P53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) [DNAY]
References: UniProt: P45481, UniProt: P04637, histone acetyltransferase
#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
111isotropic13D 1H-15N NOESY
222isotropic13D 1H-13C NOESY
131isotropic23D HN(CA)CB
165isotropic23D 1H-15N TOCSY
2107isotropic13D 1H-13C NOESY
1115isotropic13D 1H-15N NOESY
2128isotropic13D 1H-13C NOESY
1136isotropic13D 1H-15N NOESY
2143isotropic23D (H)CCH-COSY
2154isotropic23D (H)CCH-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.75 mM [U-13C; U-15N] TAZ2-p53TAD, 20 mM TRIS, 50 mM sodium chloride, 1 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2O1.5-2mM 15N labeled TAZ2-p53TAD fusion protein15N/13C_TAZ2-p53TAD_H2O90% H2O/10% D2O
solution21.75 mM [U-13C; U-15N] TAZ2-p53TAD, 20 mM [U-2H] TRIS, 50 mM sodium chloride, 1 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2O1.5-2mM 15N labeled TAZ2-p53TAD fusion protein15N/13C_TAZ2-p53TAD_D2O99% D2O, 1% H2O
solution31 mM [U-13C] TAZ2, 1 mM p53(13-37, 1 mM p53(38-61), 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 20 mM [U-2H] TRIS, 99% D2O, 1% H2OMixture of 13C TAZ2 with isolated p53TAD constructs (13-37 and 38-61)13C_TAZ2:p53(13-37/38-61)99% D2O, 1% H2O
solution41 mM TAZ2, 1 mM [U-13C] p53(13-37), 1 mM [U-13C] p53(38-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2OMixture of TAZ2 with isolated 13C p53TAD constructs (13-37 and 38-61)13C_p53(13-37/38-61):TAZ299% D2O, 1% H2O
solution51 mM TAZ2, 1 mM [U-15N] p53(13-61), 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2OMixture of TAZ2 with isolated 15N p53TAD (residues 13-61)15N_p53(13-61):TAZ290% H2O/10% D2O
solution71 mM TAZ2, 1 mM [U-13C] p53(13-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2OMixture of TAZ2 with isolated 13C p53TAD (residues 13-61)13C_p53(13-61):TAZ299% D2O, 1% H2O
solution61 mM [U-15N] TAZ2, 1 mM p53(13-61), 20 mM TRIS, 50 mM sodium chloride, 2 mM DTT, 10 % [U-2H] D2O, 90% H2O/10% D2OMixture of 15N TAZ2 with isolated p53TAD (residues 13-61)15N_TAZ2:p53(13-61)90% H2O/10% D2O
solution81 mM [U-13C] TAZ2, 1 mM p53(13-61), 20 mM [U-2H] TRIS, 50 mM sodium chloride, 2 mM [U-2H] DTT, 99 % [U-2H] D2O, 99% D2O, 1% H2OMixture of 13C TAZ2 with isolated p53TAD (residues 13-61)13C_TAZ2:p53(13-61)99% D2O, 1% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.75 mMTAZ2-p53TAD[U-13C; U-15N]1
20 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
10 %D2O[U-2H]1
1.75 mMTAZ2-p53TAD[U-13C; U-15N]2
20 mMTRIS[U-2H]2
50 mMsodium chloridenatural abundance2
1 mMDTT[U-2H]2
99 %D2O[U-2H]2
1 mMTAZ2[U-13C]3
1 mMp53(13-37natural abundance3
1 mMp53(38-61)natural abundance3
50 mMsodium chloridenatural abundance3
2 mMDTT[U-2H]3
99 %D2O[U-2H]3
20 mMTRIS[U-2H]3
1 mMTAZ2natural abundance4
1 mMp53(13-37)[U-13C]4
1 mMp53(38-61)[U-13C]4
20 mMTRIS[U-2H]4
50 mMsodium chloridenatural abundance4
2 mMDTT[U-2H]4
99 %D2O[U-2H]4
1 mMTAZ2natural abundance5
1 mMp53(13-61)[U-15N]5
20 mMTRISnatural abundance5
50 mMsodium chloridenatural abundance5
2 mMDTTnatural abundance5
10 %D2O[U-2H]5
1 mMTAZ2natural abundance7
1 mMp53(13-61)[U-13C]7
20 mMTRIS[U-2H]7
50 mMsodium chloridenatural abundance7
2 mMDTT[U-2H]7
99 %D2O[U-2H]7
1 mMTAZ2[U-15N]6
1 mMp53(13-61)natural abundance6
20 mMTRISnatural abundance6
50 mMsodium chloridenatural abundance6
2 mMDTTnatural abundance6
10 %D2O[U-2H]6
1 mMTAZ2[U-13C]8
1 mMp53(13-61)natural abundance8
20 mMTRIS[U-2H]8
50 mMsodium chloridenatural abundance8
2 mMDTT[U-2H]8
99 %D2O[U-2H]8
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMH2O_conditions6.8 1 atm305 K
250 mMD2O_conditions6.4 pD1 atm305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Initial structure generation, Refinement of CYANA structures
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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