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- PDB-2ac0: Structural Basis of DNA Recognition by p53 Tetramers (complex I) -

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Basic information

Entry
Database: PDB / ID: 2ac0
TitleStructural Basis of DNA Recognition by p53 Tetramers (complex I)
Components
  • 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'
  • Cellular tumor antigen p53
KeywordsAPOPTOSIS/DNA / Protein-DNA complex / APOPTOSIS-DNA COMPLEX
Function / homology
Function and homology information


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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase 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 / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / T cell lineage commitment / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / B cell lineage commitment / thymocyte apoptotic process / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / ER overload response / positive regulation of release of cytochrome c from mitochondria / negative regulation of DNA replication / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / Pyroptosis / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / somitogenesis / embryonic organ development / chromosome organization / T cell proliferation involved in immune response / type II interferon-mediated signaling pathway / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / positive regulation of intrinsic apoptotic signaling pathway / cellular response to glucose starvation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / mitotic G1 DNA damage checkpoint signaling / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / tumor necrosis factor-mediated signaling pathway / response to salt stress / cardiac muscle cell apoptotic process / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation
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: 1.8 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 18, 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 11, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._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
Revision 1.4Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'
F: 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'
G: 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'
H: 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,94112
Polymers104,6808
Non-polymers2624
Water18,9881054
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.439, 58.146, 77.539
Angle α, β, γ (deg.)82.93, 87.99, 73.60
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3664.380 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Cellular tumor antigen p53


Mass: 22505.582 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Ammonium Formate, PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Formate11
2PEG 335011
3H2O11
4Ammonium Formate12
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: Sep 4, 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: 1.8→40 Å / Num. all: 79253 / Num. obs: 79253 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.038 / Net I/σ(I): 24.5
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 90.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4 / Num. measured obs: 3842 / Num. unique all: 3842 / Χ2: 1.005 / % possible all: 90.6

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Processing

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

1tsr


Resolution: 1.8→33.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.611 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3896 5 %RANDOM
Rwork0.153 ---
all0.157 79253 --
obs0.157 77487 97.78 %-
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: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20.53 Å2
2---0.67 Å20.05 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 972 4 1054 8247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217450
X-RAY DIFFRACTIONr_angle_refined_deg1.7542.12810308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70822.365296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.216151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7771571
X-RAY DIFFRACTIONr_chiral_restr0.1190.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025411
X-RAY DIFFRACTIONr_nbd_refined0.2070.23421
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2977
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.2126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.271
X-RAY DIFFRACTIONr_mcbond_it2.50834071
X-RAY DIFFRACTIONr_mcangle_it3.49656469
X-RAY DIFFRACTIONr_scbond_it4.53574139
X-RAY DIFFRACTIONr_scangle_it6.206103834
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 257 -
Rwork0.181 4869 -
obs--92.96 %

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