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- PDB-2rmn: The solution structure of the p63 DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 2rmn
TitleThe solution structure of the p63 DNA-binding domain
ComponentsTumor protein 63Neoplasm
KeywordsCELL CYCLE / ANTITUMOR PROTEIN / Protein / Beta sandwich / DNA binding / p53 family / Activator / Alternative promoter usage / Apoptosis / Developmental protein / Disease mutation / DNA-binding / Ectodermal dysplasia / Metal-binding / Notch signaling pathway / Nucleus / Phosphorylation / Transcription / Transcription regulation
Function / homology
Function and homology information


ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation of cell cycle G1/S phase transition / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / WW domain binding / skin morphogenesis / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / positive regulation of Notch signaling pathway / regulation of epidermal cell division / positive regulation of stem cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / positive regulation of osteoblast differentiation / establishment of skin barrier / Pyroptosis / positive regulation of apoptotic signaling pathway / keratinocyte differentiation / Notch signaling pathway / skeletal system development / stem cell proliferation / determination of adult lifespan / TP53 Regulates Metabolic Genes / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular senescence / p53 binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / transcription by RNA polymerase II / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / dendrite / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Tumour protein p63, SAM domain / Immunoglobulin-like - #720 / 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 ...Tumour protein p63, SAM domain / Immunoglobulin-like - #720 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsEnthart, A. / Kessler, H.
CitationJournal: Sci Rep / Year: 2016
Title: Solution structure and binding specificity of the p63 DNA binding domain
Authors: Enthart, A. / Klein, C. / Dehner, A. / Coles, M. / Gemmecker, G. / Kessler, H. / Hagn, F.
History
DepositionNov 1, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9302
Polymers25,8641
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Tumor protein 63 / Neoplasm / p63 / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p51 / p40 / ...p63 / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p51 / p40 / Keratinocyte transcription factor KET / Chronic ulcerative stomatitis protein / CUSP


Mass: 25864.266 Da / Num. of mol.: 1 / Fragment: DNA binding domain, UNP residues 153-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: p20020 is as modified pQ40 vector (Klein et al., J. Biol. Chem., 276, 49020-7.)
Gene: P63 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3D4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 11 AND 12 IN THE DATABASE, P63_HUMAN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNHA
1213D HNHB
1313D 1H-15N NOESY
1423D 1H-13C NOESY
1523D CNH NOESY
1623D 1H-15N NOESY
NMR detailsText: CNH-NOESY means 13C-HSQC-NOE-15N-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM [U-15N] p63BDB; 50mM potassium chloride; 50mM potassium phosphate; 5mM DTT; 95% H2O, 5% D2O95% H2O/5% D2O
20.7mM [U-13C; U-15N] p63BDB; 50mM potassium chloride; 50mM potassium phosphate; 5mM DTT; 95% H2O, 5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMp63BDB[U-15N]1
50 mMpotassium chloride1
50 mMpotassium phosphate1
5 mMDTT1
0.7 mMp63BDB[U-13C; U-15N]2
50 mMpotassium chloride2
50 mMpotassium phosphate2
5 mMDTT2
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE9002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 21

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