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- PDB-2z5s: Molecular basis for the inhibition of p53 by Mdmx -

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Basic information

Entry
Database: PDB / ID: 2z5s
TitleMolecular basis for the inhibition of p53 by Mdmx
Components
  • Cellular tumor antigen p53
  • Mdm4 protein
KeywordsCELL CYCLE / MDMX / MDM4 / p53 / Acetylation / Activator / Anti-oncogene / Apoptosis / Cytoplasm / Disease mutation / DNA-binding / Endoplasmic reticulum / Nucleus / Phosphorylation / Polymorphism / Transcription regulation
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / 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 ...Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / 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 / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte 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 / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling
Similarity search - Function
MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 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 / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / p53-like transcription factor, DNA-binding / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellular tumor antigen p53 / Protein Mdm4 / Protein Mdm4
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPopowicz, G.M. / Czarna, A. / Rothweiler, U. / Szwagierczak, A. / Holak, T.A.
CitationJournal: Cell Cycle / Year: 2007
Title: Molecular basis for the inhibition of p53 by Mdmx.
Authors: Popowicz, G.M. / Czarna, A. / Rothweiler, U. / Szwagierczak, A. / Krajewski, M. / Weber, L. / Holak, T.A.
History
DepositionJul 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Mdm4 protein
P: Cellular tumor antigen p53
N: Mdm4 protein
Q: Cellular tumor antigen p53
O: Mdm4 protein
R: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)52,4096
Polymers52,4096
Non-polymers00
Water2,648147
1
M: Mdm4 protein
P: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)17,4702
Polymers17,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
MethodPISA
2
N: Mdm4 protein
Q: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)17,4702
Polymers17,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
MethodPISA
3
O: Mdm4 protein
R: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)17,4702
Polymers17,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.520, 30.440, 100.850
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mdm4 protein / Zebrafish MDMX


Mass: 15661.614 Da / Num. of mol.: 3 / Fragment: SWIB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdm4 / Plasmid: pET-46 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q4V944, UniProt: Q7ZUW7*PLUS
#2: Protein/peptide Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 1807.973 Da / Num. of mol.: 3 / Fragment: TRANSACTIVATION DOMAIN / Source method: obtained synthetically / Details: RP HPLC purified / References: UniProt: P04637
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 300, 0.1M MES pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 18, 2007 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 23521 / Num. obs: 21546 / % possible obs: 91.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.135
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T4F

1t4f


Resolution: 2.3→19.86 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.808 / SU B: 8.52 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.283 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3102 1121 5.1 %RANDOM
Rwork0.24743 ---
obs0.25065 20724 99.74 %-
all-21546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.253 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.01 Å2
2---0.23 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 0 147 2524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222436
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9773296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7615289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47524.717106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60815442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.971158
X-RAY DIFFRACTIONr_chiral_restr0.1380.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021785
X-RAY DIFFRACTIONr_nbd_refined0.2140.21166
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.29
X-RAY DIFFRACTIONr_mcbond_it0.6011.51516
X-RAY DIFFRACTIONr_mcangle_it1.04722395
X-RAY DIFFRACTIONr_scbond_it1.35431028
X-RAY DIFFRACTIONr_scangle_it2.1924.5901
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 77 -
Rwork0.269 1498 -
obs--99.37 %

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