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- PDB-1rg6: Solution structure of the C-terminal domain of p63 -

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Basic information

Entry
Database: PDB / ID: 1rg6
TitleSolution structure of the C-terminal domain of p63
Componentssecond splice variant p63
KeywordsGENE REGULATION / P73 SAM-LIKE DOMAIN
Function / homology
Function and homology information


positive regulation of somatic stem cell population maintenance / positive regulation of fibroblast apoptotic process / negative regulation of intracellular estrogen receptor signaling pathway / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / positive regulation of cell cycle G1/S phase transition / Developmental Lineage of Mammary Stem Cells / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / 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 somatic stem cell population maintenance / positive regulation of fibroblast apoptotic process / negative regulation of intracellular estrogen receptor signaling pathway / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / positive regulation of cell cycle G1/S phase transition / Developmental Lineage of Mammary Stem Cells / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / WW domain binding / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / regulation of epidermal cell division / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of cellular senescence / Developmental Lineage of Mammary Gland Myoepithelial Cells / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / establishment of skin barrier / positive regulation of osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / Notch signaling pathway / MDM2/MDM4 family protein binding / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / promoter-specific chromatin binding / p53 binding / regulation of apoptotic process / spermatogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / apoptotic process / positive regulation of cell population proliferation / DNA damage response / dendrite / positive regulation of DNA-templated transcription / chromatin / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Tumour protein p63, SAM domain / Transcription Factor, Ets-1 / : / 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 p63, SAM domain / Transcription Factor, Ets-1 / : / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCadot, B. / Candi, E. / Cicero, D.O. / Desideri, A. / Mele, S. / Melino, G. / Paci, M.
CitationJournal: To be Published
Title: Solution structure of the C-terminal domain of p63
Authors: Cadot, B. / Candi, E. / Cicero, D.O. / Desideri, A. / Mele, S. / Melino, G. / Paci, M.
History
DepositionNov 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: second splice variant p63


Theoretical massNumber of molelcules
Total (without water)8,5261
Polymers8,5261
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 / 500structures with the lowest energy
RepresentativeModel #19closest to the average

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Components

#1: Protein second splice variant p63


Mass: 8525.659 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 501-575)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p63 / Plasmid: pGEXsx2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9H3D4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-1H-15N TOCSY, 3D 1H-1H-15N NOESY, 3D HNHA, 2D 1H-15N HSQC
2223D HNCA, 3D HNCO, 3D CBCA(co)NH, 3D CBCANH, 3D HBHA(co)NH, H1 -C13 HSQC
3333D HACACO, 3D (H)CCH TOCSY, 3D (H)CCH TOCSY, 3D (H)CCH COSY, 3D (H)CCH COSY, 3D C13, N15 edited NOESY
4442D 1H-15N HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy and residual dipolar coupling experiment

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75mM p63 U-15N, 25mM sodium posphate, 150mM sodium chloride, 1mM AEBSF, 3mM DTT, 95% H20, 5%D2O95% H20, 5%D2O
20.25mM p63 U-15N U-13C, 25mM sodium posphate, 150mM sodium chloride, 1mM AEBSF, 3mM DTT, 95% H20, 5%D2O95% H20, 5%D2O
30.25mM p63 U-15N U-13C, 25mM sodium posphate, 150mM sodium chloride, 1mM AEBSF, 3mM DTT, 100% D2O100% D2O
40.75mM p63 U-15N, 25mM sodium posphate, 150mM sodium chloride, 1mM AEBSF, 3mM DTT, phagephage
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150mM NaCl 6ambient 298 K
2150mM NaCl 6ambient 298 K
3150mM NaCl 6ambient 298 K
4150mM NaCl 6ambient 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 AVANCEBrukerAVANCE4001
Bruker AVANCEBrukerAVANCE7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
NMRPipe970271256Delaglioprocessing
X-PLOR3.85Brungerstructure solution
NMRView5Johnsondata analysis
X-PLOR3.85Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on NOE-derived distance constraints, dihedral angle restraints, distance restraints from hydrogen bonds, costant coupling constants and residual dipolar coupling
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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