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- PDB-2ady: Structural Basis of DNA Recognition by p53 Tetramers (complex IV) -

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Basic information

Entry
Database: PDB / ID: 2ady
TitleStructural Basis of DNA Recognition by p53 Tetramers (complex IV)
Components
  • 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'
  • Cellular tumor antigen p53
KeywordsAPOPTOSIS/DNA / Protein-DNA complexes / APOPTOSIS-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 / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / viral process / Pyroptosis / 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
DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKitayner, M. / Rozenberg, H. / Kessler, N. / Rabinovich, D. / Shakked, Z.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural Basis of DNA Recognition by p53 Tetramers
Authors: Kitayner, M. / Rozenberg, H. / Kessler, N. / Rabinovich, D. / Shaulov, L. / Haran, T.E. / Shakked, Z.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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_validate_close_contact / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
E: 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'
F: 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4696
Polymers52,3384
Non-polymers1312
Water3,837213
1
E: 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'
F: 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,93812
Polymers104,6768
Non-polymers2624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)91.997, 67.903, 74.989
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Cellular tumor antigen p53


Mass: 22505.582 Da / Num. of mol.: 2 / Fragment: residues 94-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: Pet27b / Production host: Escherichia coli (E. coli) / References: UniProt: P04637
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Ammonium Fluoride, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Fluoride11
2PEG 335011
3H2O11
4Ammonium Fluoride12
5PEG 335012
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 5, 2004 / Details: Osmic Inc. MSC - Blue Confocal Mirrors
RadiationMonochromator: Osmic Inc. MSC - Blue Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→38 Å / Num. all: 16113 / Num. obs: 15517 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1029 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TSR

1tsr


Resolution: 2.5→37.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.455 / SU ML: 0.236 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 773 5 %RANDOM
Rwork0.164 ---
all0.169 16113 --
obs0.169 15517 96.31 %-
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: 36.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-1.44 Å2
2---0.68 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 486 2 213 3792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213706
X-RAY DIFFRACTIONr_angle_refined_deg1.9992.1285126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1375395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82622.381147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.08315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2021535
X-RAY DIFFRACTIONr_chiral_restr0.1090.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022697
X-RAY DIFFRACTIONr_nbd_refined0.2370.21764
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.216
X-RAY DIFFRACTIONr_mcbond_it2.41232031
X-RAY DIFFRACTIONr_mcangle_it3.90953217
X-RAY DIFFRACTIONr_scbond_it5.96172046
X-RAY DIFFRACTIONr_scangle_it8.094101908
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 51 -
Rwork0.184 973 -
obs--91.02 %

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