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- PDB-5lgy: Lysine 120-acetylated P53 DNA binding domain in a complex with th... -

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Basic information

Entry
Database: PDB / ID: 5lgy
TitleLysine 120-acetylated P53 DNA binding domain in a complex with the BAX response element.
Components
  • Cellular tumor antigen p53
  • DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3')
KeywordsTRANSCRIPTION / Acetylation / Transcription factor / Post-translational modification / Tumor suppressor / DNA binding specificity / Apoptosis / Induced fit / Genetic code expansion
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 / circadian behavior / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / homolactic fermentation / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / thymocyte apoptotic process / ER overload response / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / B cell lineage commitment / entrainment of circadian clock by photoperiod / negative regulation of mitophagy / negative regulation of DNA replication / Zygotic genome activation (ZGA) / Association of TriC/CCT with target proteins during biosynthesis / PI5P Regulates TP53 Acetylation / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / necroptotic process / positive regulation of release of cytochrome c from mitochondria / 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 / TFIID-class transcription factor complex binding / cellular response to actinomycin D / 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 / viral process / replicative senescence / general transcription initiation factor binding / 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 / Pyroptosis / positive regulation of execution phase of apoptosis / embryonic organ development / hematopoietic stem cell differentiation / response to X-ray / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / hematopoietic progenitor cell differentiation / positive regulation of cardiac muscle cell apoptotic process / core promoter sequence-specific DNA binding / glial cell proliferation / negative regulation of stem cell proliferation / cellular response to glucose starvation / negative regulation of fibroblast proliferation / mitophagy / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / positive regulation of intrinsic apoptotic signaling pathway / 14-3-3 protein binding / negative regulation of proteolysis / response to salt stress / mitotic G1 DNA damage checkpoint signaling / cardiac muscle cell apoptotic process / transcription repressor complex / gastrulation / MDM2/MDM4 family protein binding / transforming growth factor beta receptor 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 ...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 / Resolution: 2.92 Å
AuthorsArbely, E. / Vainer, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Concern Foundation United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode.
Authors: Vainer, R. / Cohen, S. / Shahar, A. / Zarivach, R. / Arbely, E.
History
DepositionJul 8, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJul 27, 2016ID: 5BUB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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: Cellular tumor antigen p53
D: Cellular tumor antigen p53
E: DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3')
F: DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,58810
Polymers102,3266
Non-polymers2624
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-76 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.703, 70.344, 104.995
Angle α, β, γ (deg.)90.00, 95.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22360.381 Da / Num. of mol.: 4 / Fragment: UNP residues 94-291
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 (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3')


Mass: 6440.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3')


Mass: 6444.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.22 M Ammonium acetate, 10% w/v PEG 3350, tri-Sodium citrate pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.92→48.65 Å / Num. obs: 21618 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.194 / Net I/σ(I): 10.9
Reflection shellResolution: 2.92→3.09 Å / Redundancy: 7.6 % / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMD

3kmd


Resolution: 2.92→43.464 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.21
RfactorNum. reflection% reflection
Rfree0.277 1049 4.87 %
Rwork0.2376 --
obs0.2395 21559 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.92→43.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6214 855 4 20 7093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117317
X-RAY DIFFRACTIONf_angle_d1.30310090
X-RAY DIFFRACTIONf_dihedral_angle_d25.3192841
X-RAY DIFFRACTIONf_chiral_restr0.0761100
X-RAY DIFFRACTIONf_plane_restr0.0121184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9169-3.07060.3691520.35972899X-RAY DIFFRACTION99
3.0706-3.26290.35621570.31582890X-RAY DIFFRACTION100
3.2629-3.51480.35831300.26992934X-RAY DIFFRACTION100
3.5148-3.86830.29781380.27252903X-RAY DIFFRACTION99
3.8683-4.42750.251450.21272947X-RAY DIFFRACTION100
4.4275-5.57640.24071700.19042925X-RAY DIFFRACTION100
5.5764-43.46920.23071570.19673012X-RAY DIFFRACTION100

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