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- PDB-3dac: Structure of the human Mdmx protein bound to the p53 tumor suppre... -

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Basic information

Entry
Database: PDB / ID: 3dac
TitleStructure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain
Components
  • Cellular tumor antigen p53P53
  • Mdm4 protein
KeywordsCELL CYCLE / MDMX / MDM4 / HDMX / HDM4 / MDM-4 / MDM-X / MDM2 / HDM2 / P53 / tumor / nucleus / oncogene / apoptosis / disease mutation / DNA-binding / transcription
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / Ub-specific processing proteases / 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 ...Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / Ub-specific processing proteases / 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 / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / 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 / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell 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 / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation
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
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPopowicz, G.M. / Czarna, A. / Holak, T.A.
CitationJournal: Cell Cycle / Year: 2008
Title: Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain.
Authors: Popowicz, G.M. / Czarna, A. / Holak, T.A.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Mdm4 protein
P: Cellular tumor antigen p53
A: Mdm4 protein
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)34,3474
Polymers34,3474
Non-polymers00
Water3,927218
1
M: Mdm4 protein
P: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)17,1732
Polymers17,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-10.9 kcal/mol
Surface area5540 Å2
MethodPISA
2
A: Mdm4 protein
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)17,1732
Polymers17,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-11.4 kcal/mol
Surface area5740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.430, 30.810, 70.090
Angle α, β, γ (deg.)90.00, 107.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mdm4 protein / / p53-binding protein Mdm4 / Mdm2-like p53-binding protein / Protein Mdmx / Double minute 4 protein


Mass: 14772.729 Da / Num. of mol.: 2 / Fragment: UNP residues 15-129 / Mutation: L46V V95L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdm4, mdmx / Plasmid: pET-46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 RIL / References: UniProt: Q7ZUW7
#2: Protein/peptide Cellular tumor antigen p53 / P53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 2400.701 Da / Num. of mol.: 2 / Fragment: UNP residues 17-37 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P04637
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2008 / Details: mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 26003 / Num. obs: 24703 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→2 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 6.9 / % possible all: 85.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCR

1ycr


Resolution: 1.8→24.49 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.707 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.124 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24292 1271 5.1 %RANDOM
Rwork0.20512 ---
obs0.2071 23573 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.09 Å2
2--0.06 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 218 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221566
X-RAY DIFFRACTIONr_bond_other_d0.0010.021040
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9762113
X-RAY DIFFRACTIONr_angle_other_deg0.8832558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8855192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84223.33357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.751156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02296
X-RAY DIFFRACTIONr_nbd_refined0.2110.2375
X-RAY DIFFRACTIONr_nbd_other0.1850.21062
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2763
X-RAY DIFFRACTIONr_nbtor_other0.0880.2712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.050.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.213
X-RAY DIFFRACTIONr_mcbond_it0.8631.51013
X-RAY DIFFRACTIONr_mcbond_other0.1431.5384
X-RAY DIFFRACTIONr_mcangle_it1.35221578
X-RAY DIFFRACTIONr_scbond_it1.7373632
X-RAY DIFFRACTIONr_scangle_it2.5754.5535
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 64 -
Rwork0.273 1341 -
obs--75.7 %

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