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- PDB-3zy0: Crystal structure of a truncated variant of the human p63 tetrame... -

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Basic information

Entry
Database: PDB / ID: 3zy0
TitleCrystal structure of a truncated variant of the human p63 tetramerization domain lacking the C-terminal helix
ComponentsTUMOR PROTEIN P63
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 / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / negative regulation of keratinocyte differentiation / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / skin morphogenesis / positive regulation of cell cycle G1/S phase transition / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / 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 / WW domain binding / hair follicle morphogenesis / regulation of epidermal cell division / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of stem cell proliferation / epithelial cell development / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / odontogenesis of dentin-containing tooth / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / keratinocyte proliferation / negative regulation of cellular senescence / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / establishment of skin barrier / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / stem cell proliferation / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / determination of adult lifespan / TP53 Regulates Metabolic Genes / promoter-specific chromatin binding / protein tetramerization / positive regulation of apoptotic signaling pathway / cellular senescence / p53 binding / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / damaged DNA binding / transcription by RNA polymerase II / 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 / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / 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, SAM 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) ...Tumour protein p63, SAM 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
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoerger, 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 / Derived calculations ...Data collection / Derived calculations / 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 / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 P63
B: TUMOR PROTEIN P63
C: TUMOR PROTEIN P63
D: TUMOR PROTEIN P63


Theoretical massNumber of molelcules
Total (without water)15,7174
Polymers15,7174
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-66.2 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.140, 33.130, 34.680
Angle α, β, γ (deg.)105.33, 102.07, 110.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
TUMOR PROTEIN P63 / 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: 3929.280 Da / Num. of mol.: 4
Fragment: TRUNCATED TETRAMERIZATION DOMAIN, RESIDUES 304-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9H3D4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 36 % / 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: 30% PEG 400, 0.1 M HEPES PH 7.5, 0.2 M MG CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→31.6 Å / Num. obs: 8661 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 9 / % possible all: 96.6

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Processing

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

Resolution: 1.9→31.55 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.994 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25231 414 4.8 %RANDOM
Rwork0.20404 ---
obs0.2064 8247 96.46 %-
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: 23.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0.05 Å2-0.31 Å2
2---0.24 Å2-1.16 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 0 50 996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4582.1091290
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4185106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.70923.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07415189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.288158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021664
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: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 27 -
Rwork0.208 609 -
obs--96.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6921-0.0563-0.56951.82970.15191.83220.03390.15030.1277-0.0746-0.06950.0233-0.121-0.09570.03570.04060.01040.01740.03150.02020.045-3.977611.290223.6647
24.2405-1.00750.90991.7231-1.16813.32050.0257-0.14230.403-0.10790.0624-0.1188-0.09920.1464-0.08810.0754-0.02110.01950.0248-0.03840.1066-10.096520.853137.0689
34.6767-1.86-0.37492.58820.57741.8902-0.0210.2822-0.2441-0.0375-0.08150.20050.027-0.14960.10250.0575-0.0259-0.01430.0514-0.00730.0436-11.46079.127925.3642
41.9822-0.8624-0.06124.40322.04224.6562-0.0313-0.2071-0.02980.1861-0.08080.10750.3343-0.06250.11210.0734-0.02680.010.0640.01550.0174-13.593215.743240.3062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 388
2X-RAY DIFFRACTION2B361 - 388
3X-RAY DIFFRACTION3C361 - 388
4X-RAY DIFFRACTION4D361 - 386

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