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- PDB-3kz8: Diversity in DNA recognition by p53 revealed by crystal structure... -

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Basic information

Entry
Database: PDB / ID: 3kz8
TitleDiversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs (p53-DNA complex 3)
Components
  • Cellular tumor antigen p53
  • DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3')
KeywordsTRANSCRIPTION/DNA / P53 / mutant protein / loop-sheet-helix motif / DNA target / activator / ANTI-oncogene apoptosis / cell cycle / covalent protein-rna linkage / disease mutation / DNA-binding / endoplasmic reticulum / glycoprotein / host-virus interaction / LI-fraumeni syndrome / methylation / nucleus / phosphoprotein / transcription / transcription regulation / transcription/dna comple / apoptosis / isopeptide bond / tumor suppressor / TRANSCRIPTION-DNA complex
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
IODIDE ION / DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRozenberg, H. / Suad, O. / Shakked, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs
Authors: Kitayner, M. / Rozenberg, H. / Rohs, R. / Suad, O. / Rabinovich, D. / Honig, B. / Shakked, Z.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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.ptnr1_auth_asym_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_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,8377
Polymers51,4523
Non-polymers3854
Water5,603311
1
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)103,67414
Polymers102,9056
Non-polymers7698
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)138.422, 49.812, 68.056
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe Hexamer is formed by chains (A, B, C, A', B', C')

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Components

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


Mass: 22505.582 Da / Num. of mol.: 2 / Fragment: P53 core domain, UNP residues 94-293
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: DNA chain DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3')


Mass: 6441.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA fragment.
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.20M AMMONIUM IODIDE, 20% PEG 3350, 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: ID23-1 / Wavelength: 0.9762 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2008 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.88→34.54 Å / Num. obs: 37958 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.099 / Net I/σ(I): 25.3
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 4.67 / Rsym value: 0.486 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.4.0078refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A of 2AC0

2ac0


Resolution: 1.91→34.54 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.908 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26642 1828 5.1 %RANDOM
Rwork0.22059 ---
obs0.223 34235 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0.45 Å2
2--0.5 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 410 4 311 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0213599
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8192.1024990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38622.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78215506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6621530
X-RAY DIFFRACTIONr_chiral_restr0.1920.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212646
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.44722016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8933286
X-RAY DIFFRACTIONr_scbond_it4.92541583
X-RAY DIFFRACTIONr_scangle_it6.50751698
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 132 -
Rwork0.291 2495 -
obs-2627 99.47 %

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