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- PDB-3zy1: Crystal structure of the human p63 tetramerization domain -

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Basic information

Entry
Database: PDB / ID: 3zy1
TitleCrystal structure of the human p63 tetramerization domain
ComponentsTUMOR PROTEIN 63Neoplasm
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / TETRAMERIZATION DOMAIN / CELL-CYCLE CONTROL
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 / 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 / establishment of skin barrier / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / MDM2/MDM4 family protein binding / Notch signaling pathway / skeletal system development / stem cell proliferation / positive regulation of apoptotic signaling pathway / determination of adult lifespan / promoter-specific chromatin binding / 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 / DNA damage response / dendrite / 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 / p53, subunit A / p53-like tetramerisation domain / 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 / p53, subunit A / p53-like tetramerisation domain / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsNatan, E. / Joerger, A.C.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structure and Kinetic Stability of the P63 Tetramerization Domain.
Authors: Natan, E. / Joerger, A.C.
History
DepositionAug 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)5,6041
Polymers5,6041
Non-polymers00
Water0
1
A: TUMOR PROTEIN 63

A: TUMOR PROTEIN 63

A: TUMOR PROTEIN 63

A: TUMOR PROTEIN 63


Theoretical massNumber of molelcules
Total (without water)22,4174
Polymers22,4174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x,-y+1,-z-11
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_554-x,y,-z-11
Buried area7870 Å2
ΔGint-66.1 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.198, 58.198, 39.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

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


Mass: 5604.372 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 398-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9H3D4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 12-15 MG/ML IN 20 MM TRIS PH 8.5, 50 MM NACL CRYSTALLIZATION BUFFER: 10% PEG 8000, 0.1 M HEPES PH 7.5, AND 0.2 M CA ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.15→58.2 Å / Num. obs: 3966 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

SoftwareName: REFMAC / Version: 5.6.0116 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.15→58.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 16.467 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28517 178 4.5 %RANDOM
Rwork0.23574 ---
obs0.23793 3785 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 81.041 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å20 Å20 Å2
2--3.54 Å20 Å2
3----7.08 Å2
Refinement stepCycle: LAST / Resolution: 2.15→58.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms332 0 0 0 332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3542.028457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.497539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.3432415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1731565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.024152
X-RAY DIFFRACTIONr_chiral_restr0.070.253
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021244
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 18 -
Rwork0.367 216 -
obs--99.57 %
Refinement TLS params.Method: refined / Origin x: 1.163 Å / Origin y: 20.5855 Å / Origin z: -15.5079 Å
111213212223313233
T0.1132 Å20.0045 Å20.0509 Å2-0.0079 Å2-0.0025 Å2--0.1201 Å2
L2.9605 °2-3.9596 °2-0.4284 °2-14.6443 °23.9803 °2--5.4131 °2
S-0.1766 Å °-0.0449 Å °-0.2309 Å °0.7616 Å °0.1467 Å °-0.0662 Å °-0.0567 Å °0.0235 Å °0.0298 Å °

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