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- PDB-2iom: Mouse p53 core domain soaked with 2-propanol -

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Basic information

Entry
Database: PDB / ID: 2iom
TitleMouse p53 core domain soaked with 2-propanol
ComponentsCellular tumor antigen p53
KeywordsTRANSCRIPTION / ANTITUMOR PROTEIN / IG Fold
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / PI5P Regulates TP53 Acetylation / RUNX3 regulates CDKN1A transcription / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Stabilization of p53 ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / PI5P Regulates TP53 Acetylation / RUNX3 regulates CDKN1A transcription / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Stabilization of p53 / Regulation of TP53 Activity through Methylation / Regulation of TP53 Degradation / Oncogene Induced Senescence / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Ovarian tumor domain proteases / PKR-mediated signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / The role of GTSE1 in G2/M progression after G2 checkpoint / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Ub-specific processing proteases / negative regulation of G1 to G0 transition / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / oxidative stress-induced premature senescence / positive regulation of thymocyte apoptotic process / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / mRNA transcription / entrainment of circadian clock by photoperiod / hematopoietic stem cell differentiation / positive regulation of release of cytochrome c from mitochondria / negative regulation of telomere maintenance via telomerase / replicative senescence / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TFIID-class transcription factor complex binding / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / response to X-ray / positive regulation of execution phase of apoptosis / negative regulation of fibroblast proliferation / type II interferon-mediated signaling pathway / core promoter sequence-specific DNA binding / determination of adult lifespan / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / MDM2/MDM4 family protein binding / protein phosphatase 2A binding / transcription initiation-coupled chromatin remodeling / molecular function activator activity / tumor necrosis factor-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator / cellular response to ionizing radiation / mRNA 3'-UTR binding / cellular response to xenobiotic stimulus / nucleotide-excision repair / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / circadian rhythm / cellular response to gamma radiation / negative regulation of cell growth / receptor tyrosine kinase binding / PML body / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular senescence / positive regulation of reactive oxygen species metabolic process / transcription coactivator binding / histone deacetylase binding / autophagy / nuclear matrix / disordered domain specific binding / intracellular protein localization / cellular response to UV / p53 binding / positive regulation of cellular senescence / protein-folding chaperone binding / protease binding / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ras protein signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / negative regulation of cell population proliferation / copper ion binding / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding
Similarity search - Function
Immunoglobulin-like - #720 / 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 ...Immunoglobulin-like - #720 / 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
ISOPROPYL ALCOHOL / Cellular tumor antigen p53
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHo, W.C. / Luo, C. / Zhao, K. / Chai, X. / Fitzgerald, M.X. / Marmorstein, R.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds.
Authors: Ho, W.C. / Luo, C. / Zhao, K. / Chai, X. / Fitzgerald, M.X. / Marmorstein, R.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,0624
Polymers22,8141
Non-polymers2483
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.299, 44.541, 62.915
Angle α, β, γ (deg.)90.00, 126.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellular tumor antigen p53 / Tumor suppressor p53


Mass: 22814.057 Da / Num. of mol.: 1 / Fragment: mouse p53 core domain, residues 92-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tp53, P53, Trp53 / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02340
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / pH: 7
Details: 100mM Tris, 16-18% PEG 2K MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 92.2 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57269 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.1
Reflection shellResolution: 2→50 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.92

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å
RfactorNum. reflection
Rfree0.246 13740
Rwork0.209 -
obs0.209 57269
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 9 161 1642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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