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- PDB-7dvd: The crystal structure of p53 DNA binding domain and PUMA complex -

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Basic information

Entry
Database: PDB / ID: 7dvd
TitleThe crystal structure of p53 DNA binding domain and PUMA complex
Components
  • Bcl-2-binding component 3, isoforms 1/2
  • Cellular tumor antigen p53
KeywordsPEPTIDE BINDING PROTEIN / p53 PUMA BH3 peptide complex
Function / homology
Function and homology information


positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / 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 / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / fibroblast apoptotic process / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / 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 / 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 / execution phase of apoptosis / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / FOXO-mediated transcription of cell death genes / PI5P Regulates TP53 Acetylation / positive regulation of IRE1-mediated unfolded protein response / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / 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 / rRNA transcription / 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 / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / 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 / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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 ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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
Similarity search - Domain/homology
Cellular tumor antigen p53 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsHan, C.W. / Lee, H.N. / Jeong, M.S. / Jang, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1D1A1B07043701 Korea, Republic Of
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural basis of the p53 DNA binding domain and PUMA complex.
Authors: Han, C.W. / Lee, H.N. / Jeong, M.S. / Park, S.Y. / Jang, S.B.
#1: Journal: Biochem Biophys Res Commun. / Year: 2012
Title: In vitro binding properties of tumor suppressor p53 with PUMA and NOXA
Authors: Park, S.Y. / Jang, S.B.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Bcl-2-binding component 3, isoforms 1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8549
Polymers94,5925
Non-polymers2624
Water1,60389
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2952
Polymers23,2291
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10020 Å2
MethodPISA
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2952
Polymers23,2291
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-3 kcal/mol
Surface area10250 Å2
MethodPISA
3
C: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2952
Polymers23,2291
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10230 Å2
MethodPISA
4
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2952
Polymers23,2291
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-4 kcal/mol
Surface area10090 Å2
MethodPISA
5
E: Bcl-2-binding component 3, isoforms 1/2


Theoretical massNumber of molelcules
Total (without water)1,6751
Polymers1,6751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.612, 73.411, 84.408
Angle α, β, γ (deg.)89.939, 89.823, 89.996
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 23229.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Zn / Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#2: Protein/peptide Bcl-2-binding component 3, isoforms 1/2 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 1674.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.66 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris (pH 7.0) 20% (w/w) PEG-200 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 62203 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.24 Å2 / CC1/2: 0.915 / Net I/σ(I): 13.506
Reflection shellResolution: 2.5904→2.635 Å / Rmerge(I) obs: 0.323 / Num. unique obs: 2327

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Processing

Software
NameVersionClassification
HKL-20001.14_3260data collection
PHENIX1.11.1_2575data processing
Cootdata scaling
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WXR

2wxr


Resolution: 2.59→26.28 Å / SU ML: 0.3853 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.8173 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3177 2756 5.43 %
Rwork0.2699 48027 -
obs0.2726 50783 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.84 Å2
Refinement stepCycle: LAST / Resolution: 2.59→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6319 0 4 89 6412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00936464
X-RAY DIFFRACTIONf_angle_d1.14298771
X-RAY DIFFRACTIONf_chiral_restr0.0611961
X-RAY DIFFRACTIONf_plane_restr0.00741161
X-RAY DIFFRACTIONf_dihedral_angle_d8.94783961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.630.35571140.25692213X-RAY DIFFRACTION88.21
2.63-2.680.36111230.28882356X-RAY DIFFRACTION98.96
2.68-2.730.36111080.28052486X-RAY DIFFRACTION99.43
2.73-2.790.38971720.29892386X-RAY DIFFRACTION99.77
2.79-2.850.35871200.28722406X-RAY DIFFRACTION99.8
2.85-2.920.36291020.27922429X-RAY DIFFRACTION99.84
2.92-2.990.36511310.28152451X-RAY DIFFRACTION99.85
2.99-3.070.31231570.2692370X-RAY DIFFRACTION99.92
3.07-3.160.28971320.27532444X-RAY DIFFRACTION99.88
3.16-3.260.36081040.26452471X-RAY DIFFRACTION100
3.26-3.380.41121270.28642428X-RAY DIFFRACTION100
3.38-3.510.2778990.25822466X-RAY DIFFRACTION100
3.51-3.670.26221160.23912419X-RAY DIFFRACTION99.84
3.67-3.870.3071510.272435X-RAY DIFFRACTION99.92
3.87-4.110.33591470.27512381X-RAY DIFFRACTION100
4.11-4.420.29121590.26732378X-RAY DIFFRACTION99.84
4.42-4.870.28911690.26172422X-RAY DIFFRACTION99.77
4.87-5.560.27271600.25162387X-RAY DIFFRACTION99.61
5.56-6.990.36231880.29462355X-RAY DIFFRACTION99.84
6.99-26.280.29371770.27042344X-RAY DIFFRACTION98.52

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