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- PDB-5mf7: New Insights into the Role of DNA Shape on Its Recognition by p53... -

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Basic information

Entry
Database: PDB / ID: 5mf7
TitleNew Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-GADD45)
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 / 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 / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / 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 / rRNA transcription / negative regulation of reactive oxygen species metabolic process / 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 / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of execution phase of apoptosis / 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
DI(HYDROXYETHYL)ETHER / 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: 1.59 Å
AuthorsRozenberg, H. / Diskin-Posner, Y. / 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 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / struct / struct_conn / struct_conn_type
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 1.3Jan 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)51,7106
Polymers51,4733
Non-polymers2373
Water8,323462
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)103,42112
Polymers102,9476
Non-polymers4746
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)138.056, 50.034, 67.202
Angle α, β, γ (deg.)90.000, 92.520, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: PET27-B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P04637
#2: DNA chain DNA


Mass: 6462.196 Da / Num. of mol.: 1 / Fragment: DNA / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: PEG / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.25 Å3/Da / Density % sol: 45.39 % / Mosaicity: 0.605 °
Crystal growTemperature: 292 K / Method: evaporation / pH: 8 / Details: 4% Tacsimate, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 75213 / % possible obs: 98 % / Redundancy: 8 % / Biso Wilson estimate: 14.56 Å2 / Rmerge(I) obs: 0.102 / Net I/av σ(I): 19.798 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.48-1.516.51.5330.714193.1
1.51-1.537.51.4070.798197
1.53-1.567.81.1530.859197.2
1.56-1.5980.9380.91197.2
1.59-1.638.10.8610.926197.4
1.63-1.678.10.6920.945197.6
1.67-1.718.10.5590.962197.6
1.71-1.758.20.4410.976198
1.75-1.818.20.3580.987198
1.81-1.868.20.2840.99198.1
1.86-1.938.20.2130.993198.2
1.93-2.018.20.1680.996198.4
2.01-2.18.20.1380.997198.5
2.1-2.218.20.110.998198.7
2.21-2.358.10.0950.998198.7
2.35-2.538.10.0830.998199.1
2.53-2.798.10.0760.998199.2
2.79-3.198.10.0610.999199.4
3.19-4.0280.0480.998199.5
4.02-507.80.0470.999199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.01 Å49.2 Å
Translation5.01 Å49.2 Å

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Processing

Software
NameVersionClassification
PHENIXdev-2499_1692refinement
PHASER2.7.3phasing
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: 1.59→49.199 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.08
Details: Translational non-crystallographic symmetry (tNCS) correction
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 4207 6.93 %RANDOM SELECTION
Rwork0.1984 ---
obs0.2008 60700 98.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.7 Å2 / Biso mean: 23.2305 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 1.59→49.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 574 9 464 3953
Biso mean--26.4 31.51 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014138
X-RAY DIFFRACTIONf_angle_d1.0735820
X-RAY DIFFRACTIONf_chiral_restr0.066639
X-RAY DIFFRACTIONf_plane_restr0.007636
X-RAY DIFFRACTIONf_dihedral_angle_d18.8332398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.60810.34461460.33281863200997
1.6081-1.6270.32951340.30731851198597
1.627-1.64680.36341300.28781847197797
1.6468-1.66770.26591380.27651857199597
1.6677-1.68960.29861410.26781839198097
1.6896-1.71280.31851440.26311895203998
1.7128-1.73720.27171400.25881824196498
1.7372-1.76320.27981280.24651865199398
1.7632-1.79070.26241680.2491889205798
1.7907-1.82010.27171170.23241880199798
1.8201-1.85150.28581420.22651859200198
1.8515-1.88510.29091360.22871864200098
1.8851-1.92140.23841490.23321873202298
1.9214-1.96060.25971340.20761854198898
1.9606-2.00330.2561460.21531885203198
2.0033-2.04990.25191400.22161868200898
2.0499-2.10110.28571500.2121890204098
2.1011-2.15790.2251300.20711904203499
2.1579-2.22140.25171370.20421864200199
2.2214-2.29310.20361400.19291884202499
2.2931-2.37510.26051420.20051925206799
2.3751-2.47020.21421390.19981891203099
2.4702-2.58260.22951380.19761886202499
2.5826-2.71870.27581440.19231897204199
2.7187-2.88910.2871450.21191929207499
2.8891-3.11210.24021450.1941906205199
3.1121-3.42520.20541450.17061923206899
3.4252-3.92070.20641440.153219332077100
3.9207-4.93890.15141430.133619602103100
4.9389-49.22270.14141320.15331888202094
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05570.00390.01060.00040.00560.23040.0006-0.03480.04050.01160.0005-0.06130.0097-0.0602-0.03030.0872-0.0124-0.04850.1460.02220.289632.47310.168319.5125
20.077-0.01740.03070.0105-0.01060.0215-0.02610.0035-0.0046-0.0203-0.03960.01520.0063-0.00010.00030.21230.0264-0.00260.18070.03350.188120.41659.7124.6586
30.1796-0.16180.00960.4969-0.2380.2955-0.0651-0.0219-0.00770.0099-0.0101-0.11590.05410.0116-0.68630.06410.02580.02890.0538-0.00030.059920.90511.978314.4411
40.026-0.02420.03650.0285-0.02080.0810.0095-0.0092-0.04980.00330.0119-0.04940.0469-0.07040.00240.0729-0.03260.02180.1287-0.05330.21426.5213-7.959412.426
50.1811-0.12710.03810.3809-0.04060.2715-0.0342-0.00340.1127-0.0235-0.0447-0.01870.0437-0.052-0.34310.07940.0112-0.01310.0533-0.03760.111920.23130.287513.043
60.01850.0025-0.05370.0004-0.00730.1557-0.041-0.00840.05970.11350.0575-0.11030.0159-0.0087-0.06050.12820.0251-0.00730.10440.0670.233230.98180.172953.0853
70.0319-0.00860.00940.0031-0.0040.0083-0.02350.0034-0.0049-0.0183-0.03770.01190.006-0.000300.20540.02680.00690.19190.02960.18118.93839.709838.2356
80.25740.00140.0060.1151-0.1510.2482-0.0666-0.00660.10560.0448-0.0451-0.1515-0.06310.0083-0.59330.0657-0.0151-0.04680.09910.02220.137919.4522.01247.8832
90.00750.0080.00140.0090.00080.00130.01780.0006-0.09020.01410.0092-0.05110.0295-0.10360.00030.1740.01650.02950.11520.00810.09235.0394-7.963346.0001
100.0183-0.04810.04720.1795-0.02780.3005-0.01340.05440.02320.0176-0.0626-0.08950.00610.0501-0.49670.07170.03290.0180.12890.05140.067319.8164-3.473646.1986
110.0101-0.008-0.01580.00680.01340.02830.06730.00150.0414-0.01310.0016-0.0135-0.02810.00090.04260.1758-0.0203-0.03810.10620.05550.277213.868720.328349.0662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 94 through 112 )A94 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 123 )A113 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 176 )A124 - 176
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 194 )A177 - 194
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 293 )A195 - 293
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 112 )B94 - 112
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 123 )B113 - 123
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 176 )B124 - 176
9X-RAY DIFFRACTION9chain 'B' and (resid 177 through 194 )B177 - 194
10X-RAY DIFFRACTION10chain 'B' and (resid 195 through 277 )B195 - 277
11X-RAY DIFFRACTION11chain 'B' and (resid 278 through 293 )B278 - 293

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