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- PDB-3d08: Human p53 core domain with hot spot mutation R249S and second-sit... -

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Basic information

Entry
Database: PDB / ID: 3d08
TitleHuman p53 core domain with hot spot mutation R249S and second-site suppressor mutation H168R
ComponentsCellular tumor antigen p53
KeywordsTRANSCRIPTION / p53 / Mutant Protein / Loop-sheet-helix motif / Acetylation / Activator / Alternative splicing / Anti-oncogene / Apoptosis / Cell cycle / Covalent protein-RNA linkage / Cytoplasm / Disease mutation / DNA-binding / Endoplasmic reticulum / Glycoprotein / Host-virus interaction / Li-Fraumeni syndrome / Metal-binding / Methylation / Nucleus / Phosphoprotein / Polymorphism / Transcription regulation / Ubl conjugation / Zinc
Function / homology
Function and homology information


negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / bone marrow development / positive regulation of programmed necrotic cell death / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / negative regulation of mitophagy / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / cellular response to UV-C / replicative senescence / general transcription initiation factor binding / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / neuroblast proliferation / Pyroptosis / viral process / hematopoietic stem cell differentiation / response to X-ray / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / glial cell proliferation / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / mitophagy / cis-regulatory region sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / response to salt stress / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / negative regulation of proteolysis / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex / intrinsic apoptotic signaling pathway
Similarity search - Function
Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / 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 / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSuad, O. / Rozenberg, H. / Shimon, L.J.W. / Frolow, F. / Shakked, Z.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations
Authors: Suad, O. / Rozenberg, H. / Brosh, R. / Diskin-Posner, Y. / Kessler, N. / Shimon, L.J.W. / Frolow, F. / Liran, A. / Rotter, V. / Shakked, Z.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5202
Polymers22,4551
Non-polymers651
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.287, 46.287, 327.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 22454.514 Da / Num. of mol.: 1 / Fragment: p53 Core Domain, UNP residues 94-293 / Mutation: R249S, H168R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53 / Plasmid: pET27-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.2M Sodium acetate, 20% PEG3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2005 / Details: Cylindrical grazing incidence mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 1.4→34.2 Å / Num. all: 41783 / Num. obs: 41783 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 30.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 8.9 / Num. unique all: 1686 / Rsym value: 0.23 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREP- CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TSR

1tsr


Resolution: 1.4→34.2 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.903 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21189 2088 5 %RANDOM
Rwork0.1984 ---
all0.1991 41783 --
obs0.1991 39658 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.908 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 1 231 1741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221559
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.9662139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85922.53767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5711516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021204
X-RAY DIFFRACTIONr_nbd_refined0.2040.2687
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2169
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.216
X-RAY DIFFRACTIONr_mcbond_it2.14131002
X-RAY DIFFRACTIONr_mcangle_it3.07351608
X-RAY DIFFRACTIONr_scbond_it3.7237620
X-RAY DIFFRACTIONr_scangle_it5.06110517
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 132 -
Rwork0.214 2429 -
obs-2561 83.88 %

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