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- PDB-5n2o: Structure Of P63 SAM Domain L514F Mutant Causative Of AEC Syndrome -

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Basic information

Entry
Database: PDB / ID: 5n2o
TitleStructure Of P63 SAM Domain L514F Mutant Causative Of AEC Syndrome
ComponentsTumor protein 63
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / PROTEIN
Function / homology
Function and homology information


skin epidermis development / : / Regulation of TP53 Activity through Association with Co-factors / : / ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / regulation of cysteine-type endopeptidase activity involved in apoptotic process / prostatic bud formation ...skin epidermis development / : / Regulation of TP53 Activity through Association with Co-factors / : / ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / regulation of cysteine-type endopeptidase activity involved in apoptotic process / prostatic bud formation / negative regulation of mesoderm development / anatomical structure formation involved in morphogenesis / 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 / epidermal cell differentiation / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / morphogenesis of a polarized epithelium / prostate gland development / proximal/distal pattern formation / positive regulation of cell cycle G1/S phase transition / positive regulation of fibroblast apoptotic process / multicellular organism development / WW domain binding / cranial skeletal system development / skin morphogenesis / pattern specification process / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / embryonic limb morphogenesis / hair follicle development / hair follicle morphogenesis / positive regulation of Notch signaling pathway / regulation of epidermal cell division / epithelial cell development / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / keratinocyte proliferation / epithelial cell differentiation / epidermis development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / establishment of skin barrier / positive regulation of osteoblast differentiation / keratinocyte differentiation / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Notch signaling pathway / positive regulation of apoptotic signaling pathway / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / protein tetramerization / p53 binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / neuron apoptotic process / sequence-specific DNA binding / cell population proliferation / damaged DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / DNA damage response / dendrite / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Tumour protein p63 / 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 / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsRinnenthal, J. / Wuerz, J.M. / Osterburg, C. / Guentert, P. / Doetsch, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDO 545/8-1 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Protein aggregation of the p63 transcription factor underlies severe skin fragility in AEC syndrome.
Authors: Russo, C. / Osterburg, C. / Sirico, A. / Antonini, D. / Ambrosio, R. / Wurz, J.M. / Rinnenthal, J. / Ferniani, M. / Kehrloesser, S. / Schafer, B. / Guntert, P. / Sinha, S. / Dotsch, V. / Missero, C.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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)7,9581
Polymers7,9581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5340 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Tumor protein 63 / p63 / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L


Mass: 7957.985 Da / Num. of mol.: 1 / Mutation: L14F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tp63, P63, P73l, Tp73l, Trp63 / Production host: Escherichia coli (E. coli) / References: UniProt: O88898

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic23D 1H-15N TOCSY
131isotropic23D 1H-15N NOESY
142isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1350 uM [U-13C; U-15N] Tumor protein 63, 95% H2O/5% D2O15N_13C_p63SAML514F95% H2O/5% D2O
solution2350 uM Tumor protein 63, 100% D2ONA_p63SAML514F_D2Oex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMTumor protein 63[U-13C; U-15N]1
350 uMTumor protein 63natural abundance2
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 7 / Pressure: AMBIENT Pa / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxdata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 9
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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