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- PDB-4a9z: CRYSTAL STRUCTURE OF HUMAN P63 TETRAMERIZATION DOMAIN -

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Basic information

Entry
Database: PDB / ID: 4a9z
TitleCRYSTAL STRUCTURE OF HUMAN P63 TETRAMERIZATION DOMAIN
ComponentsTUMOR PROTEIN 63Neoplasm
KeywordsTRANSCRIPTION
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsMuniz, J.R.C. / Coutandin, D. / Salah, E. / Chaikuad, A. / Vollmar, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Dotsch, V. ...Muniz, J.R.C. / Coutandin, D. / Salah, E. / Chaikuad, A. / Vollmar, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Dotsch, V. / von Delft, F. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of Human P63 Tetramerization Domain
Authors: Muniz, J.R.C. / Coutandin, D. / Salah, E. / Chaikuad, A. / Vollmar, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Dotsch, V. / von Delft, F. / Knapp, S.
History
DepositionNov 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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

Downloads & links

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Assembly

Deposited unit
A: TUMOR PROTEIN 63
B: TUMOR PROTEIN 63
C: TUMOR PROTEIN 63
D: TUMOR PROTEIN 63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8765
Polymers29,5214
Non-polymers3541
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-61.4 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.850, 80.850, 68.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3613, -0.833, -0.419), (-0.8098, -0.5031, 0.3019), (-0.4623, 0.2302, -0.8563)
Vector: 61.0659, 90.5323, 20.574)

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Components

#1: Protein
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: 7380.309 Da / Num. of mol.: 4 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 397-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H3D4
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.01 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→70.02 Å / Num. obs: 11980 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 10.2 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→48.92 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.212
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 572 4.78 %RANDOM
Rwork0.1944 ---
obs0.1967 11961 99.96 %-
Displacement parametersBiso mean: 66.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.0136 Å20 Å20 Å2
2--0.0136 Å20 Å2
3----0.0273 Å2
Refine analyzeLuzzati coordinate error obs: 0.335 Å
Refinement stepCycle: LAST / Resolution: 2.29→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 12 45 1677
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011684HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.982274HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d829SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes229HARMONIC5
X-RAY DIFFRACTIONt_it1684HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion3.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion215SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1920SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.51 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2117 128 4.56 %
Rwork0.1999 2680 -
all0.2004 2808 -
obs--99.96 %
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)
16.6341.1621-1.58777.70892.22060.33040.1771-0.38820.6050.0388-0.1022-0.0892-0.1150.1002-0.0748-0.083-0.01850.10280.0105-0.010.031145.287337.95338.5693
26.3464-0.4675-1.10077.1184-3.91434.6918-0.09740.3675-0.0603-0.09130.2932-0.4163-0.0827-0.1503-0.1958-0.1577-0.07450.0396-0.1166-0.1197-0.059347.838327.18964.0401
34.3448-0.75093.8893-0.8629-0.98124.6112-0.0559-0.1381-0.21840.28260.0622-0.2967-0.01530.1527-0.00620.08540.0466-0.14370.0168-0.0550.136963.381115.536512.0952
49.09-0.2834-0.59026.93413.00321.80660.09470.24990.2796-0.3151-0.0052-0.1579-0.2824-0.1187-0.0895-0.1731-0.00990.1069-0.03210.0685-0.037542.687336.79921.955
59.71310.4897-2.90982.4263-0.05473.913-0.0601-0.00420.67740.02160.0923-0.2373-0.17810.2018-0.0322-0.0941-0.09950.0942-0.1285-0.12110.106553.912138.61390.3674
6-0.71790.4704-1.28130.78250.78292.4577-0.05670.32170.0513-0.20940.0124-0.00990.03970.010.04430.05680.06930.15120.3278-0.0882-0.189764.613234.9258-16.8001
73.6003-1.81930.7461.4231-0.05018.31550.07960.0679-0.2202-0.1332-0.10280.00360.15850.58030.0233-0.186-0.0390.01560.1712-0.11510.094665.356419.9806-5.1633
86.5851.6907-1.96753.4036-2.40127.3706-0.08630.05580.0650.281-0.0092-0.2010.21140.68830.0955-0.0842-0.0436-0.084-0.1116-0.0689-0.054759.487623.08855.1607
9-0.86860.11430.0842.2411-0.34225.861-0.0344-0.0171-0.27150.2305-0.02670.47040.0977-0.5720.061-0.2009-0.12880.07660.06770.05380.105337.978423.88137.8143
10-0.86320.3939-0.45221.23632.589400.0050.0451-0.0916-0.07540.0160.04670.0944-0.0321-0.0211-0.0602-0.07070.00490.19890.0126-0.063534.976127.781-4.3151
114.727-1.15492.73582.2506-1.78122.98320.0358-0.0346-0.0905-0.1370.1533-0.03660.10080.6814-0.1891-0.1505-0.0106-0.04280.1077-0.05760.076569.928125.6456-2.5496
124.81273.1472-1.01967.8999-2.25793.40.25570.02020.49160.16910.00160.2371-0.48850.3464-0.2573-0.0572-0.16390.0525-0.1059-0.0828-0.084458.514736.9804-5.6347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 358:368
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 369:387
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 388:404
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 358:368
5X-RAY DIFFRACTION5CHAIN B AND RESSEQ 369:387
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 388:402
7X-RAY DIFFRACTION7CHAIN C AND RESSEQ 358:368
8X-RAY DIFFRACTION8CHAIN C AND RESSEQ 369:389
9X-RAY DIFFRACTION9CHAIN C AND RESSEQ 390:410
10X-RAY DIFFRACTION10CHAIN C AND RESSEQ 411:415
11X-RAY DIFFRACTION11CHAIN D AND RESSEQ 358:368
12X-RAY DIFFRACTION12CHAIN D AND RESSEQ 369:401

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