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- PDB-2geq: Crystal Structure of a p53 Core Dimer Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 2geq
TitleCrystal Structure of a p53 Core Dimer Bound to DNA
Components
  • 5'-D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3'
  • Cellular tumor antigen p53P53
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / Tumor Suppressor / TRANSCRIPTION-DNA COMPLEX
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 / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / 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 / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / 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 / regulation of cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Ub-specific processing proteases / negative regulation of DNA biosynthetic process / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / embryo development ending in birth or egg hatching / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of leukocyte migration / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TFIID-class transcription factor complex binding / mitophagy / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / negative regulation of mitotic cell cycle / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / somitogenesis / positive regulation of cell cycle / type II interferon-mediated signaling pathway / regulation of neuron apoptotic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
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 / p53-like tetramerisation domain superfamily ...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
DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHo, W.C. / Fitzgerald, M.X. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the p53 Core Domain Dimer Bound to DNA.
Authors: Ho, W.C. / Fitzgerald, M.X. / Marmorstein, R.
History
DepositionMar 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3'
D: 5'-D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3'
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8028
Polymers55,4264
Non-polymers3754
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.755, 94.290, 119.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*GP*CP*GP*TP*GP*AP*GP*CP*AP*TP*GP*CP*TP*CP*AP*C)-3'


Mass: 4899.179 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Cellular tumor antigen p53 / P53 / Tumor suppressor p53


Mass: 22814.057 Da / Num. of mol.: 2 / Fragment: p53 core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tp53, P53, Trp53 / Plasmid: pRSET A / Production host: Escherichia coli (E. coli) / References: UniProt: P02340
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M NH4Cl, 0.01 M CaCl2, 0.05 M Tris-HCl, 28% Peg 4000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1NH4Cl11
2CaCl211
3Tris-HClTris11
4Peg 400011
5H2O11
6NH4Cl12
7CaCl212
8Peg 400012
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91756 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91756 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 23284 / % possible obs: 96.1 % / Redundancy: 4.2 % / Rsym value: 0.056 / Net I/σ(I): 20.1
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.43 / Num. unique all: 2109 / Rsym value: 0.252 / % possible all: 89.3

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TSR

1tsr


Resolution: 2.3→47.15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 98647.523 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1152 5.3 %RANDOM
Rwork0.202 ---
obs-21916 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.006 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---5.4 Å20 Å2
3---6.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 574 18 236 3833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.243 107 5.6 %
Rwork0.253 1813 -
obs-1920 84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5trs_xplor_par.txttrs_xplor_top.txt

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