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- PDB-5mg7: New Insights into the Role of DNA Shape on Its Recognition by p53... -

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Basic information

Entry
Database: PDB / ID: 5mg7
TitleNew Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-p53R2)
Components
  • Cellular tumor antigen p53
  • DNA
KeywordsTRANSCRIPTION / P53 / TRANSCRIPTION FACTOR / DNA BINDING / DNA RECOGNITION / HOOGSTEEN BASE-PAIRING / TRANSCRIPTION REGULATION / APOPTOSIS / BIOLOGICAL RHYTHMS / CELL CYCLE / NUCLEUS / TUMOR SUPPRESSOR / ANTIGEN NY-CO-13 / PHOSPHOPROTEIN
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / 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 / mRNA transcription / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / hematopoietic progenitor cell differentiation / negative regulation of telomere maintenance via telomerase / 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 in response to DNA damage by p53 class mediator / replicative senescence / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / 14-3-3 protein binding / response to gamma radiation / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / DNA damage response, signal transduction by p53 class mediator / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / mRNA 3'-UTR binding / Regulation of NF-kappa B signaling / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / Stabilization of p53 / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / cellular senescence / PML body / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / transcription coactivator binding / intracellular protein localization / positive regulation of reactive oxygen species metabolic process / histone deacetylase binding
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 ...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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsRozenberg, H. / Braeuning, B. / Golovenko, D. / Shakked, Z.
CitationJournal: Structure / Year: 2018
Title: New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins.
Authors: Golovenko, D. / Brauning, B. / Vyas, P. / Haran, T.E. / Rozenberg, H. / Shakked, Z.
History
DepositionNov 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.3Oct 30, 2019Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5565
Polymers51,4253
Non-polymers1312
Water9,296516
1
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: DNA
hetero molecules

A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,11210
Polymers102,8516
Non-polymers2624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)137.621, 49.804, 68.089
Angle α, β, γ (deg.)90.000, 93.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 22505.582 Da / Num. of mol.: 2 / Fragment: P53 DNA Binding Domain, UNP Residues 94-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637
#2: DNA chain DNA


Mass: 6414.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESISED BY IDT / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 7
Details: 0.07 M ammonium tartrate dibasic, 8.4% Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 82061 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 12.04 Å2 / Rmerge(I) obs: 0.091 / Net I/av σ(I): 20.796 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.45-1.484.41.0110.804198.5
1.48-1.55.10.8860.8771100
1.5-1.535.60.7590.9141100
1.53-1.5660.6240.9481100
1.56-1.66.10.5220.9631100
1.6-1.636.20.4360.9721100
1.63-1.676.20.3570.9811100
1.67-1.726.30.2820.9871100
1.72-1.776.30.230.991100
1.77-1.836.20.190.9931100
1.83-1.896.30.1590.9931100
1.89-1.976.20.1290.9961100
1.97-2.066.20.1090.9961100
2.06-2.176.20.090.9971100
2.17-2.36.10.080.9971100
2.3-2.486.10.0760.9971100
2.48-2.7360.070.9971100
2.73-3.125.90.0620.9971100
3.12-3.945.90.050.998199.9
3.94-506.20.0480.998199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.69 Å38.92 Å
Translation4.69 Å38.92 Å

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Processing

Software
NameVersionClassification
PHENIXdev_2264refinement
PHASER2.6.1phasing
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2AC0

2ac0


Resolution: 1.45→27.768 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.43
Details: Translational non-crystallographic symmetry (tNCS) correction
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 4025 4.99 %RANDOM SELECTION
Rwork0.1709 ---
obs0.1724 80697 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.25 Å2 / Biso mean: 18.8805 Å2 / Biso min: 4.57 Å2
Refinement stepCycle: final / Resolution: 1.45→27.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 492 2 526 4081
Biso mean--11.51 30.31 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094316
X-RAY DIFFRACTIONf_angle_d1.176059
X-RAY DIFFRACTIONf_chiral_restr0.093658
X-RAY DIFFRACTIONf_plane_restr0.007675
X-RAY DIFFRACTIONf_dihedral_angle_d20.6811705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4495-1.46650.3327910.29571873196470
1.4665-1.48440.32061500.270725962746100
1.4844-1.50320.25941390.256726662805100
1.5032-1.5230.23821310.243326542785100
1.523-1.54380.25261500.23426612811100
1.5438-1.56590.27041340.220626822816100
1.5659-1.58930.25971470.204726542801100
1.5893-1.61410.23991350.190226632798100
1.6141-1.64060.22351310.19326382769100
1.6406-1.66880.21741530.185726762829100
1.6688-1.69920.24351400.183126822822100
1.6992-1.73190.22721370.181326482785100
1.7319-1.76720.22281460.170826572803100
1.7672-1.80560.22671370.174526722809100
1.8056-1.84760.20541370.173426752812100
1.8476-1.89380.19791460.166926492795100
1.8938-1.9450.18451430.16626832826100
1.945-2.00220.23831370.159526882825100
2.0022-2.06680.20481430.159726842827100
2.0668-2.14070.19181370.163426552792100
2.1407-2.22630.1991460.157826932839100
2.2263-2.32760.2191310.162726592790100
2.3276-2.45030.17721450.166727002845100
2.4503-2.60370.18571460.168626982844100
2.6037-2.80450.19361310.167426912822100
2.8045-3.08640.21131420.170327042846100
3.0864-3.53230.1751480.147726912839100
3.5323-4.44740.18411420.138427332875100
4.4474-27.77340.13781300.15682647277794

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