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- PDB-5hoc: p73 homo-tetramerization domain mutant II -

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Basic information

Entry
Database: PDB / ID: 5hoc
Titlep73 homo-tetramerization domain mutant II
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: 1.36007789334 Å
AuthorsCoutandin, D. / Krojer, T. / Salah, E. / Mathea, S. / Sumyk, M. / Knapp, S. / Dotsch, V.
CitationJournal: Cell Death Differ. / Year: 2016
Title: Mechanism of TAp73 inhibition by Delta Np63 and structural basis of p63/p73 hetero-tetramerization.
Authors: Gebel, J. / Luh, L.M. / Coutandin, D. / Osterburg, C. / Lohr, F. / Schafer, B. / Frombach, A.S. / 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 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Tumor protein p73
B: Tumor protein p73


Theoretical massNumber of molelcules
Total (without water)12,0982
Polymers12,0982
Non-polymers00
Water63135
1
A: Tumor protein p73
B: Tumor protein p73

A: Tumor protein p73
B: Tumor protein p73


Theoretical massNumber of molelcules
Total (without water)24,1954
Polymers24,1954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8470 Å2
ΔGint-61 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.149, 60.149, 61.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n

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Components

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


Mass: 6048.816 Da / Num. of mol.: 2 / Fragment: UNP residues 351-398 / Mutation: E363R, K370E, E373R, R390D
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M Sodium chloride, 0.1 M sodium phosphate, 0.1 M potassium phosphate , 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.36→60.15 Å / Num. obs: 24811 / % possible obs: 99.8 % / Redundancy: 9.8 % / Biso Wilson estimate: 18.3967383267 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.021 / Net I/σ(I): 16.3 / Num. measured all: 244067 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.36-1.426.20.4652.61827829610.8140.19499.7
4.71-60.1512.30.07636.787147110.9940.023100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DIALSdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WQI

2wqi


Resolution: 1.36007789334→43.0234569038 Å / SU ML: 0.143322310631 / Cross valid method: FREE R-VALUE / σ(F): 1.32650981721 / Phase error: 26.8804389251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246759091983 1198 4.82850348636 %
Rwork0.23272701562 23613 -
obs0.233418540806 24811 99.666586326 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.3926703997 Å2
Refinement stepCycle: LAST / Resolution: 1.36007789334→43.0234569038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 0 35 735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00989240314861722
X-RAY DIFFRACTIONf_angle_d1.03815555355978
X-RAY DIFFRACTIONf_chiral_restr0.0744975959126112
X-RAY DIFFRACTIONf_plane_restr0.00630063152509127
X-RAY DIFFRACTIONf_dihedral_angle_d13.4130650241276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3601-1.41450.3551467323071460.3172097582282538X-RAY DIFFRACTION99.333826795
1.4145-1.47890.2966153266331350.2884001303612549X-RAY DIFFRACTION98.9675516224
1.4789-1.55690.2717957360331370.2498727285392563X-RAY DIFFRACTION99.4475138122
1.5569-1.65440.2848861699621400.2549168795462577X-RAY DIFFRACTION99.8529952223
1.6544-1.78220.2276004767241200.2391258166872624X-RAY DIFFRACTION99.9271667881
1.7822-1.96150.2903605130551010.2364052214532639X-RAY DIFFRACTION99.9270605398
1.9615-2.24540.2200530321221260.226656456952646X-RAY DIFFRACTION99.7840172786
2.2454-2.82880.2592438619391480.2325071145542652X-RAY DIFFRACTION99.9286224126
2.8288-43.0450.2305344691011450.221705499352825X-RAY DIFFRACTION99.8990918264

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