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- PDB-2wqj: Crystal structure of a truncated variant of the human p73 tetrame... -

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Basic information

Entry
Database: PDB / ID: 2wqj
TitleCrystal structure of a truncated variant of the human p73 tetramerization domain
ComponentsTUMOR PROTEIN P73
KeywordsTRANSCRIPTION / P73 / P63 / P53 / TUMOR SUPPRESSION / TRANSCRIPTION FACTOR / TETRAMER / HEXAMER / 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 / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of neuron differentiation / digestive tract morphogenesis ...positive regulation of lung ciliated cell differentiation / cerebrospinal fluid secretion / negative regulation of cardiac muscle cell proliferation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of neuron differentiation / digestive tract morphogenesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of oligodendrocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of cell size / neuron development / mismatch repair / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / release of cytochrome c from mitochondria / transcription corepressor binding / post-embryonic development / hippocampus development / protein tetramerization / kidney development / 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 / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of MAPK cascade / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / inflammatory response / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / centrosome / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tumour protein p73, 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 p73, 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: 2 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

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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
I: TUMOR PROTEIN P73
J: TUMOR PROTEIN P73
K: TUMOR PROTEIN P73
L: TUMOR PROTEIN P73
M: TUMOR PROTEIN P73
N: TUMOR PROTEIN P73
O: TUMOR PROTEIN P73
P: TUMOR PROTEIN P73
Q: TUMOR PROTEIN P73
R: TUMOR PROTEIN P73
S: TUMOR PROTEIN P73
T: TUMOR PROTEIN P73
U: TUMOR PROTEIN P73
V: TUMOR PROTEIN P73
W: TUMOR PROTEIN P73
X: TUMOR PROTEIN P73
Y: TUMOR PROTEIN P73
Z: TUMOR PROTEIN P73
1: TUMOR PROTEIN P73
2: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)117,00528
Polymers117,00528
Non-polymers00
Water8,125451
1
G: TUMOR PROTEIN P73
H: TUMOR PROTEIN P73
I: TUMOR PROTEIN P73
J: TUMOR PROTEIN P73
K: TUMOR PROTEIN P73
L: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-79.67 kcal/mol
Surface area9220 Å2
MethodPISA
2
A: TUMOR PROTEIN P73
B: TUMOR PROTEIN P73
C: TUMOR PROTEIN P73
D: TUMOR PROTEIN P73
E: TUMOR PROTEIN P73
F: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-73.53 kcal/mol
Surface area10120 Å2
MethodPISA
3
S: TUMOR PROTEIN P73
T: TUMOR PROTEIN P73
U: TUMOR PROTEIN P73
V: TUMOR PROTEIN P73
W: TUMOR PROTEIN P73
X: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-80.48 kcal/mol
Surface area9330 Å2
MethodPISA
4
M: TUMOR PROTEIN P73
N: TUMOR PROTEIN P73
O: TUMOR PROTEIN P73
P: TUMOR PROTEIN P73
Q: TUMOR PROTEIN P73
R: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)25,0726
Polymers25,0726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-73.62 kcal/mol
Surface area9750 Å2
MethodPISA
5
Y: TUMOR PROTEIN P73
Z: TUMOR PROTEIN P73
1: TUMOR PROTEIN P73
2: TUMOR PROTEIN P73


Theoretical massNumber of molelcules
Total (without water)16,7154
Polymers16,7154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-49.2 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.850, 98.930, 120.120
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 4178.738 Da / Num. of mol.: 28
Fragment: TRUNCATED TETRAMERIZATION DOMAIN, RESIDUES 351-383
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


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP VAPOR DIFFUSION AT 17 DEGREE C. PROTEIN SOLUTION: 10 MG/ML IN 20 MM TRIS (PH 8.5), 50 MM NACL. CRYSTALLIZATION BUFFER: 0.1 M TRIS (PH 8.5), 0.9 M AMMONIUM PHOSPHATE.

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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: 2→76.4 Å / Num. obs: 90937 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3

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Processing

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

Resolution: 2→24.96 Å / SU ML: 0.29 / σ(F): 1.08 / Phase error: 25.49 / Stereochemistry target values: ML
Details: THIS ENTRY REPORTS THE STRUCTURE OF A TRUNCATED FORM OF THE P73 TETRAMERIZATION DOMAIN (RESIDUES 351-383)THAT LACKS A C-TERMINAL HELIX THAT IS ESSENTIAL FOR STABILIZING THE OVERALL ...Details: THIS ENTRY REPORTS THE STRUCTURE OF A TRUNCATED FORM OF THE P73 TETRAMERIZATION DOMAIN (RESIDUES 351-383)THAT LACKS A C-TERMINAL HELIX THAT IS ESSENTIAL FOR STABILIZING THE OVERALL ARCHITECTURE OF THE P73 TETRAMER. SEE PDB ENTRY 2WQI WITH THE STRUCTURE OF P73 RESIDUES 351-399 FOR COMPARISON.
RfactorNum. reflection% reflection
Rfree0.2484 8569 4.9 %
Rwork0.2103 --
obs0.2123 173614 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.14 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.9256 Å20 Å2-1.0093 Å2
2--3.6417 Å20 Å2
3----6.5673 Å2
Refinement stepCycle: LAST / Resolution: 2→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 0 451 7100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066711
X-RAY DIFFRACTIONf_angle_d0.8928939
X-RAY DIFFRACTIONf_dihedral_angle_d15.0762620
X-RAY DIFFRACTIONf_chiral_restr0.055997
X-RAY DIFFRACTIONf_plane_restr0.0031120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.31432240.27115290X-RAY DIFFRACTION94
2.0227-2.04650.29162660.26415412X-RAY DIFFRACTION95
2.0465-2.07150.30322700.26775406X-RAY DIFFRACTION94
2.0715-2.09770.29792740.24115357X-RAY DIFFRACTION95
2.0977-2.12530.2342910.23345424X-RAY DIFFRACTION95
2.1253-2.15440.28512870.23325412X-RAY DIFFRACTION95
2.1544-2.18510.26593280.22875312X-RAY DIFFRACTION95
2.1851-2.21770.31043100.24045469X-RAY DIFFRACTION95
2.2177-2.25230.25222480.23315448X-RAY DIFFRACTION95
2.2523-2.28920.33192570.23715504X-RAY DIFFRACTION96
2.2892-2.32870.25992400.23845442X-RAY DIFFRACTION96
2.3287-2.3710.3083360.23365405X-RAY DIFFRACTION96
2.371-2.41660.25842760.22695525X-RAY DIFFRACTION96
2.4166-2.46590.28352780.2235431X-RAY DIFFRACTION96
2.4659-2.51940.2642880.22635539X-RAY DIFFRACTION96
2.5194-2.5780.28182960.22255455X-RAY DIFFRACTION97
2.578-2.64240.23952730.21255512X-RAY DIFFRACTION97
2.6424-2.71370.27992770.2155513X-RAY DIFFRACTION97
2.7137-2.79350.25642620.21315595X-RAY DIFFRACTION97
2.7935-2.88350.25812830.21165519X-RAY DIFFRACTION97
2.8835-2.98640.25222870.21985530X-RAY DIFFRACTION97
2.9864-3.10580.26612900.22315608X-RAY DIFFRACTION98
3.1058-3.24680.223040.21055541X-RAY DIFFRACTION98
3.2468-3.41760.23673320.19275599X-RAY DIFFRACTION99
3.4176-3.63110.19983100.17035603X-RAY DIFFRACTION99
3.6311-3.91050.21513200.17445577X-RAY DIFFRACTION99
3.9105-4.30230.21013040.17675606X-RAY DIFFRACTION99
4.3023-4.92070.19832970.17075666X-RAY DIFFRACTION99
4.9207-6.18390.2632750.21915671X-RAY DIFFRACTION99
6.1839-24.96240.26262860.22765674X-RAY DIFFRACTION99

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