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- PDB-3exj: Crystal Structure of a p53 Core Tetramer Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3exj
TitleCrystal Structure of a p53 Core Tetramer Bound to DNA
Components
  • 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
  • 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
  • mouse p53 core domain
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / Acetylation / Activator / Anti-oncogene / Apoptosis / Cell cycle / Covalent protein-RNA linkage / Cytoplasm / Disease mutation / DNA-binding / Endoplasmic reticulum / Metal-binding / Methylation / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Zinc / 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 / 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
CITRATE ANION / DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMalecka, K.A.
CitationJournal: Oncogene / Year: 2009
Title: Crystal structure of a p53 core tetramer bound to DNA.
Authors: Malecka, K.A. / Ho, W.C. / Marmorstein, R.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Remark 999The complete crystallized DNA sequence is 5'-TTGAGCATGCTCGAGCATGCTCA-3'. The sequence in the ...The complete crystallized DNA sequence is 5'-TTGAGCATGCTCGAGCATGCTCA-3'. The sequence in the asymmetric unit is only half of the complete sequence (GAGCATGCTCA for chain C and GAGCATGTCTC for chain D. The biological unit isgenerated by applying the (-X, Y, -Z) symmetry.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mouse p53 core domain
B: mouse p53 core domain
C: 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0997
Polymers51,7794
Non-polymers3203
Water10,413578
1
A: mouse p53 core domain
B: mouse p53 core domain
C: 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules

A: mouse p53 core domain
B: mouse p53 core domain
C: 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,19714
Polymers103,5578
Non-polymers6406
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4470 Å2
ΔGint-48 kcal/mol
Surface area22440 Å2
Unit cell
Length a, b, c (Å)114.740, 68.016, 75.162
Angle α, β, γ (deg.)90.00, 111.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein mouse p53 core domain


Mass: 22383.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P02340

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: p53 consensus sequence
#3: DNA chain 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'


Mass: 3653.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: p53 consensus sequence

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Non-polymers , 3 types, 581 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200 mM lithium citrate, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Lithium Citrate11
2PEG 335011
3Lithium Citrate12
4PEG 335012

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorDate: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→70.186 Å / Num. obs: 36093 / Redundancy: 4.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.5
Reflection shellHighest resolution: 2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.7 Å / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
Rfree0.26 -
Rwork0.225 -
obs-36093
Refinement stepCycle: LAST / Resolution: 2→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 468 15 578 4128

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