[English] 日本語
Yorodumi
- PDB-2ac0: Structural Basis of DNA Recognition by p53 Tetramers (complex I) -

+
Open data


ID or keywords:

Loading...

-
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 p53P53
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 / 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 / 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 / RUNX3 regulates CDKN1A transcription / germ cell nucleus / 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 / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / 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 / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / 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 / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1054 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more