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- PDB-2kby: The Tetramerization Domain of Human p73 -

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Basic information

Entry
Database: PDB / ID: 2kby
TitleThe Tetramerization Domain of Human p73
ComponentsTumor protein p73
KeywordsTRANSCRIPTION / tetramerization domain / Activator / Alternative splicing / Anti-oncogene / Apoptosis / Cell cycle / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription regulation / Ubl conjugation / Zinc
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mismatch repair / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Tumour protein p73, SAM domain / p53, subunit A / p53-like tetramerisation domain / 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 ...Tumour protein p73, SAM domain / p53, subunit A / p53-like tetramerisation domain / 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 / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsCoutandin, D. / Ikeya, T. / Loehr, F. / Guntert, P. / Ou, H.D. / Doetsch, V.
CitationJournal: Cell Death Differ. / Year: 2009
Title: Conformational stability and activity of p73 require a second helix in the tetramerization domain.
Authors: Coutandin, D. / Lohr, F. / Niesen, F.H. / Ikeya, T. / Weber, T.A. / Schafer, B. / Zielonka, E.M. / Bullock, A.N. / Yang, A. / Guntert, P. / Knapp, S. / McKeon, F. / Ou, H.D. / Dotsch, V.
History
DepositionDec 12, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 29, 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_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73


Theoretical massNumber of molelcules
Total (without water)24,1394
Polymers24,1394
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Tumor protein p73 / p53-like transcription factor / p53-related protein


Mass: 6034.828 Da / Num. of mol.: 4 / Fragment: tetramerization domain, UNP residues 351-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P73, TP73 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / References: UniProt: O15350

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-1H NOESY
1233D NOESY-[15N,1H]-TROSY
2313D NOESY-[13C,1H]-HSQC
1423D NOESY-[13C,1H]-HSQC
2554D-CT-J-Resolved 13C-separated NOESY
1643D 15N-edited/13C-separated NOESY
1743D 15N/13C-separated NOESY
1823D HN(CA)CB
1923D HN(CO)CA
11023D HNCO
11123D H(CCO)NH
11223D C(CO)NH
1133TOCSY-[15N,1H]-TROSY
1146CT-[13C,1H]-HSQC
3157C-coupled HA(CACO)NH
3167F2-IPAP-CT-[13C,1H]-HSQC
3177[15N,1H]-TROSY/anti-TROSY
3187HN-TROSY IPAP
3197C-coupled HNCO
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5mM [U-13C; U-15N] p73 TD-1, 20mM sodium phosphate-2, 100mM sodium chloride-3, 100% D2O100% D2O
22.5mM [U-13C; U-15N] p73 TD-4, 20mM sodium phosphate-5, 100mM sodium chloride-6, 95% H2O/5% D2O95% H2O/5% D2O
32.5mM [U-15N] p73 TD-7, 20mM sodium phosphate-8, 100mM sodium chloride-9, 95% H2O/5% D2O95% H2O/5% D2O
42.5mM [U-15N] p73 TD-10, 2.5mM [U-13C] p73 TD-11, 20mM sodium phosphate-12, 100mM sodium chloride-13, 95% H2O/5% D2O95% H2O/5% D2O
52.5mM [U-15N] p73 TD-14, 2.5mM [U-13C] p73 TD-15, 20mM sodium phosphate-16, 100mM sodium chloride-17, 100% D2O100% D2O
62.5mM [U-10% 13C] p73 TD-18, 20mM sodium phosphate-19, 100mM sodium chloride-20, 95% H2O/5% D2O95% H2O/5% D2O
72.5mM [U-13C; U-15N] p73 TD-21, 16.4 Hz Pf1 phage-22, 50mM arginine-23, 50mM glutamate-24, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMp73 TD-1[U-13C; U-15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
2.5 mMp73 TD-4[U-13C; U-15N]2
20 mMsodium phosphate-52
100 mMsodium chloride-62
2.5 mMp73 TD-7[U-15N]3
20 mMsodium phosphate-83
100 mMsodium chloride-93
2.5 mMp73 TD-10[U-15N]4
2.5 mMp73 TD-11[U-13C]4
20 mMsodium phosphate-124
100 mMsodium chloride-134
2.5 mMp73 TD-14[U-15N]5
2.5 mMp73 TD-15[U-13C]5
20 mMsodium phosphate-165
100 mMsodium chloride-175
2.5 mMp73 TD-18[U-10% 13C]6
20 mMsodium phosphate-196
100 mMsodium chloride-206
2.5 mMp73 TD-21[U-13C; U-15N]7
16.4 mMPf1 phage-227
50 mMarginine-237
50 mMglutamate-247
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 1 atm303 K
21 atm303 K
36.8 1 atm303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue, Nilgesautomatic assignment
ARIA2.2Linge, O'Donoghue, Nilgesstructure solution
ARIA2.2Linge, O'Donoghue, Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2529 / NOE intraresidue total count: 445 / NOE long range total count: 14 / NOE medium range total count: 188 / NOE sequential total count: 261 / Hydrogen bond constraints total count: 26 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 39 / Protein psi angle constraints total count: 40
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.013 Å / Distance rms dev error: 0.004 Å

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