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- PDB-2y9u: Structural basis of p63a SAM domain mutants involved in AEC syndrome -

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Basic information

Entry
Database: PDB / ID: 2y9u
TitleStructural basis of p63a SAM domain mutants involved in AEC syndrome
ComponentsTUMOR PROTEIN 63
KeywordsAPOPTOSIS / STERILE ALPHA MOTIF / 5-HELIX BUNDLE / MUTATIONS / AEC SYNDROME
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 / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / 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 / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of stem cell proliferation / 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 / establishment of skin barrier / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / stem cell proliferation / skeletal system development / determination of adult lifespan / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / positive regulation of apoptotic signaling pathway / 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 / DNA damage response / chromatin binding / dendrite / 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 / nucleus / metal ion binding / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: TUMOR PROTEIN 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0012
Polymers7,9051
Non-polymers961
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.624, 38.309, 44.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TUMOR PROTEIN 63 / 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: 7904.923 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN, RESIDUES 545-611
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.13 % / Description: NONE
Crystal growpH: 6.4
Details: 100 MM SODIUM CITRATE, PH 6.4, 500MM LITHIUM SULPHATE, 500MM AMMONIUM SULPHATE, 5MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→27.4 Å / Num. obs: 8205 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 15.69 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14
Reflection shellHighest resolution: 1.6 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.7 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.249 Å / SU ML: 0.16 / σ(F): 1.32 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 757 5.2 %
Rwork0.1853 --
obs0.1863 8175 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.799 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5086 Å20 Å20 Å2
2--1.1207 Å20 Å2
3----6.7947 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 0 5 81 630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009562
X-RAY DIFFRACTIONf_angle_d1.192761
X-RAY DIFFRACTIONf_dihedral_angle_d16.183194
X-RAY DIFFRACTIONf_chiral_restr0.07384
X-RAY DIFFRACTIONf_plane_restr0.00595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.72360.2251660.20022782X-RAY DIFFRACTION97
1.7236-1.89690.20171670.18492777X-RAY DIFFRACTION97
1.8969-2.17120.22141500.17682794X-RAY DIFFRACTION97
2.1712-2.73470.23061360.18122793X-RAY DIFFRACTION97
2.7347-22.25090.18171380.18382782X-RAY DIFFRACTION97

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