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- PDB-2y9t: Structural basis of p63a SAM domain mutants involved in AEC syndrome -

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Basic information

Entry
Database: PDB / ID: 2y9t
TitleStructural basis of p63a SAM domain mutants involved in AEC syndrome
ComponentsTUMOR PROTEIN 63Neoplasm
KeywordsAPOPTOSIS / STERILE ALPHA MOTIF / 5-HELIX BUNDLE
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 / skin morphogenesis / WW domain binding / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / epithelial cell development / 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 / positive regulation of osteoblast differentiation / MDM2/MDM4 family protein binding / establishment of skin barrier / Pyroptosis / positive regulation of apoptotic signaling pathway / Notch signaling pathway / keratinocyte differentiation / 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 / dendrite / apoptotic process / 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 / 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 ...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 / CNS
AuthorsSathyamurthy, A. / Freund, S.M.V. / Johnson, C.M. / Allen, M.D.
CitationJournal: FEBS J. / Year: 2011
Title: Structural Basis of P63Alpha Sam Domain Mutants Involved in Aec Syndrome.
Authors: Sathyamurthy, A. / Freund, S.M.V. / Johnson, C.M. / Allen, M.D. / Bycroft, M.
History
DepositionFeb 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR PROTEIN 63


Theoretical massNumber of molelcules
Total (without water)9,3311
Polymers9,3311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS > 0.25A
Representative

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Components

#1: Protein TUMOR PROTEIN 63 / Neoplasm / CHRONIC ULCERATIVE STOMATITIS PROTEIN / KERATINOCYTE TRANSCRIPTION FACTOR KET / TRANSFORMATION- ...CHRONIC ULCERATIVE STOMATITIS PROTEIN / KERATINOCYTE TRANSCRIPTION FACTOR KET / TRANSFORMATION-RELATED PROTEIN 63 / TUMOR PROTEIN P73-LIKE / P40 / P51 / P63 / CUSP / TP63 / P73L


Mass: 9330.511 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN, RESIDUES 543-622
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9H3D4
Sequence detailsGLY AND SER AND THE N-TERMINUS ARE FROM THE FUSION TAG

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIGstructure solution
CNSstructure solution
RefinementMethod: CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATIONS > 0.25A / Conformers calculated total number: 20 / Conformers submitted total number: 20

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