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- PDB-2fej: Solution structure of human p53 DNA binding domain. -

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Basic information

Entry
Database: PDB / ID: 2fej
TitleSolution structure of human p53 DNA binding domain.
ComponentsCellular tumor antigen p53
KeywordsTRANSCRIPTION / BETA SANDWICH
Function / homology
Function and homology information


negative regulation of helicase activity / 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 / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / 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 / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / positive regulation of execution phase of apoptosis / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / hematopoietic stem cell differentiation / Pyroptosis / viral process / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / positive regulation of cardiac muscle cell apoptotic process / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / mitotic G1 DNA damage checkpoint signaling / response to salt stress / 14-3-3 protein binding / negative regulation of proteolysis / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
Similarity search - Function
Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPerez-Canadillas, J.M. / Tidow, H. / Freund, S.M. / Rutherford, T.J. / Ang, H.C. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Solution structure of p53 core domain: Structural basis for its instability
Authors: Perez-Canadillas, J.M. / Tidow, H. / Freund, S.M. / Rutherford, T.J. / Ang, H.C. / Fersht, A.R.
History
DepositionDec 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0742
Polymers23,0081
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)36 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 23008.105 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9NP68, UniProt: P04637*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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 NOESY
1213D 15N-separated NOESY
1322D NOESY
1423D 13C-separated NOESY
1532D NOESY
1633D 13C-separated NOESY
1742D NOESY
1852D NOESY
1962D NOESY
11072D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM p53 core U-15N,13C, 2H; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.3 mM p53 core U-15N,13C, 2H + reverse ILV 13CH3 ; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
30.3 mM p53 core U-15N,13C, 2H + reverse ILV 13CH3 + reverse Tyr ; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 100% D2O100% D2O
40.3 mM p53 core U-15N,13C, 2H + Met and Phe (1H); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
50.3 mM p53 core U-15N,13C, 2H + Met and Arg (1H); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
60.4 mM p53 core U-15N,13C, 2H (50%); 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
70.4 mM p53 core N/A; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
80.4 mM p53 core N/A; 25 mM Tris-HCl pH 7.1; 150 mM NaCl; 100% D2O100% D2O
Sample conditionsIonic strength: 150 mM / pH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE8002
Bruker DRXBrukerDRX5003

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Processing

NMR softwareName: CNS / Version: 1 / Developer: Brunger et al / Classification: data analysis
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: 50 / Conformers submitted total number: 36

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