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- PDB-2wqi: Crystal structure of the human p73 tetramerization domain -

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Basic information

Entry
Database: PDB / ID: 2wqi
TitleCrystal structure of the human p73 tetramerization domain
ComponentsTUMOR PROTEIN P73P73
KeywordsTRANSCRIPTION / P73 / P63 / P53 / TUMOR SUPPRESSION / TRANSCRIPTION FACTOR / TETRAMER / OLIGOMERIZATION DOMAIN / DNA-BINDING / COOPERATIVITY / CELL-CYCLE CONTROL / TRANSCRIPTION REGULATION / APOPTOSIS / CELL CYCLE / DEVELOPMENT
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 / MAD / Resolution: 1.7 Å
AuthorsJoerger, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural Evolution of P53, P63, and P73: Implication for Heterotetramer Formation.
Authors: Joerger, A.C. / Rajagopalan, S. / Natan, E. / Veprintsev, D.B. / Robinson, C.V. / Fersht, A.R.
History
DepositionAug 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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 1.4May 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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
C: TUMOR PROTEIN P73
D: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)24,5284
Polymers24,5284
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-65.76 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.110, 76.110, 79.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
TUMOR PROTEIN P73 / P73 / P53-LIKE TRANSCRIPTION FACTOR / P53-RELATED PROTEIN / P73


Mass: 6131.942 Da / Num. of mol.: 4 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 351-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O15350
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTWO ADDITIONAL N-TERMINAL RESIDUES (GS, CLONING TAG)

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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: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 15 MG/ML IN 20 MM TRIS (PH 8.5), 50 MM NACL. CRYSTALLIZATION BUFFER: 0.1 M SODIUM CITRATE (PH 6.2), 40% PEG 600.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50.8 Å / Num. obs: 18950 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 26.19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.7→23.78 Å / SU ML: 0.22 / σ(F): 2.02 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1921 5.1 %
Rwork0.209 --
obs0.211 37829 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.74 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.9122 Å20 Å20 Å2
2---5.9122 Å2-0 Å2
3---11.8244 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 0 113 1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051485
X-RAY DIFFRACTIONf_angle_d0.9812002
X-RAY DIFFRACTIONf_dihedral_angle_d15.944574
X-RAY DIFFRACTIONf_chiral_restr0.059228
X-RAY DIFFRACTIONf_plane_restr0.004257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.26671360.24262566X-RAY DIFFRACTION100
1.7425-1.78960.25741320.2392575X-RAY DIFFRACTION100
1.7896-1.84220.23751400.21812603X-RAY DIFFRACTION100
1.8422-1.90170.3021560.23352568X-RAY DIFFRACTION100
1.9017-1.96960.28131320.23742569X-RAY DIFFRACTION100
1.9696-2.04840.26351260.22962549X-RAY DIFFRACTION100
2.0484-2.14160.25841660.20942564X-RAY DIFFRACTION100
2.1416-2.25440.19471300.20172540X-RAY DIFFRACTION100
2.2544-2.39560.28061380.19642544X-RAY DIFFRACTION100
2.3956-2.58030.22951180.21262603X-RAY DIFFRACTION100
2.5803-2.83960.25891480.22442566X-RAY DIFFRACTION100
2.8396-3.24960.30571520.21922518X-RAY DIFFRACTION100
3.2496-4.09080.2661340.18482574X-RAY DIFFRACTION100
4.0908-23.77870.19031130.19542569X-RAY DIFFRACTION99

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