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- PDB-5hob: p73 homo-tetramerization domain mutant I -

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Basic information

Entry
Database: PDB / ID: 5hob
Titlep73 homo-tetramerization domain mutant I
ComponentsTumor protein p73P73
KeywordsTRANSCRIPTION / transcription factor / tetramerization domain / p73 / homo-tetramerization mutant / hetero-tetramerization
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / mismatch repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cell cycle / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Tumour protein p73, 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 p73, 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: 1.22001298703 Å
AuthorsCoutandin, D. / Krojer, T. / Salah, E. / Mathea, S. / Knapp, S. / Dotsch, V.
CitationJournal: To Be Published
Title: Structural basis of p63/p73 hetero-tetramerization
Authors: Gebel, J. / Luh, L. / Coutandin, D. / Lohr, F. / Schafer, B. / Sumyk, M. / Buchner, L. / Krojer, T. / Salah, E. / Mathea, S. / Guntert, P. / Knapp, S. / Dotsch, V.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73
E: Tumor protein p73
F: Tumor protein p73
G: Tumor protein p73
H: Tumor protein p73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3039
Polymers48,2798
Non-polymers241
Water6,774376
1
A: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73


Theoretical massNumber of molelcules
Total (without water)24,1394
Polymers24,1394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-62 kcal/mol
Surface area10480 Å2
MethodPISA
2
E: Tumor protein p73
F: Tumor protein p73
G: Tumor protein p73
H: Tumor protein p73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1645
Polymers24,1394
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-74 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.050, 48.400, 75.730
Angle α, β, γ (deg.)89.600, 83.200, 74.270
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide
Tumor protein p73 / P73 / p53-like transcription factor / p53-related protein


Mass: 6034.828 Da / Num. of mol.: 8 / Fragment: tetramerization domain, UNP residues 351-398 / Mutation: E363K, K370E, E373R, R390E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP73, P73 / Production host: Escherichia coli (E. coli) / References: UniProt: O15350
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% w/v PEG Smear Medium, 0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 5 % 2-propanol, 10 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.22→46.57 Å / Num. obs: 79962 / % possible obs: 68.1 % / Redundancy: 2 % / Biso Wilson estimate: 17.0365125277 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.8
Reflection shellResolution: 1.22→1.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.508 / % possible all: 8.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WQI

2wqi


Resolution: 1.22001298703→46.57 Å / SU ML: 0.122690638506 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 31.4965846917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214185206205 4012 5.01744600493 %
Rwork0.188357509707 75949 -
obs0.189632559259 79961 68.1371588285 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.5301185703 Å2
Refinement stepCycle: LAST / Resolution: 1.22001298703→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 1 376 3288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912528035332962
X-RAY DIFFRACTIONf_angle_d1.049354752294000
X-RAY DIFFRACTIONf_chiral_restr0.0707220504726458
X-RAY DIFFRACTIONf_plane_restr0.00583147827302516
X-RAY DIFFRACTIONf_dihedral_angle_d15.17739761031151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.23440.3475424667960.314291889213241X-RAY DIFFRACTION6.07775590551
1.2344-1.24940.270494726067150.307161291041374X-RAY DIFFRACTION9.84311740891
1.2494-1.26520.293601164156300.29416794166473X-RAY DIFFRACTION12.3678387017
1.2652-1.28190.421985045029290.278613676093622X-RAY DIFFRACTION16.2384634572
1.2819-1.29940.264901762178330.284243700514763X-RAY DIFFRACTION19.688350235
1.2994-1.3180.335010650066390.268882904389965X-RAY DIFFRACTION24.6743671664
1.318-1.33770.30071227359570.2686742446031065X-RAY DIFFRACTION27.8342842967
1.3377-1.35860.262946788987760.2651204950991295X-RAY DIFFRACTION34.1299477222
1.3586-1.38090.291623198557790.2569016391661608X-RAY DIFFRACTION41.1363082175
1.3809-1.40470.259189707298870.2568031519321753X-RAY DIFFRACTION46.0345258944
1.4047-1.43020.2840454919121230.2465674409812110X-RAY DIFFRACTION55.0678175092
1.4302-1.45770.2880621072441360.245448518062591X-RAY DIFFRACTION66.9859985262
1.4577-1.48750.2586326114151690.2226341142243244X-RAY DIFFRACTION85.2184769039
1.4875-1.51980.2143185865741880.2144645145353606X-RAY DIFFRACTION93.5865811544
1.5198-1.55520.2330418809051940.2104520121213599X-RAY DIFFRACTION94.0257808627
1.5552-1.59410.2233462032031880.2154363096473647X-RAY DIFFRACTION94.8084054388
1.5941-1.63720.2388674578971930.2218598493743630X-RAY DIFFRACTION94.5117428925
1.6372-1.68540.2320130390481740.2186575845263689X-RAY DIFFRACTION94.7742885182
1.6854-1.73980.227589282281950.211791681973629X-RAY DIFFRACTION95.3378209923
1.7398-1.8020.2342724760681940.2085480518543716X-RAY DIFFRACTION95.5756538744
1.802-1.87410.2170411695431960.203929150823624X-RAY DIFFRACTION95.3331669578
1.8741-1.95940.2245387508022030.2115481229073685X-RAY DIFFRACTION95.6692913386
1.9594-2.06270.2159104735292150.1882073850593656X-RAY DIFFRACTION95.7694210787
2.0627-2.19190.1897791803222020.170159964013678X-RAY DIFFRACTION96.0158376639
2.1919-2.36120.1969197778761880.1707031329473739X-RAY DIFFRACTION96.7956618191
2.3612-2.59880.2043750600371920.1784983042583740X-RAY DIFFRACTION96.942800789
2.5988-2.97480.1964152920932350.1904123241153696X-RAY DIFFRACTION97.591857001
2.9748-3.74760.2178679867812130.172812992853737X-RAY DIFFRACTION97.4586725882
3.7476-46.60530.2085124996241630.1753993972313774X-RAY DIFFRACTION97.3300370828

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