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- PDB-7el4: The crystal structure of p53p peptide fragment in complex with th... -

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Basic information

Entry
Database: PDB / ID: 7el4
TitleThe crystal structure of p53p peptide fragment in complex with the N-terminal domain of MdmX
ComponentsCellular tumor antigen p53,Protein Mdm4
KeywordsONCOPROTEIN / p53 / MdmX / SIGNALING PROTEIN
Function / homology
Function and homology information


atrial septum development / ventricular septum development / atrioventricular valve morphogenesis / heart valve development / endocardial cushion morphogenesis / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / signal transduction by p53 class mediator ...atrial septum development / ventricular septum development / atrioventricular valve morphogenesis / heart valve development / endocardial cushion morphogenesis / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / circadian behavior / cellular response to actinomycin D / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / 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 / mRNA transcription / Urea cycle / Regulation of TP53 Activity through Association with Co-factors / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / 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 / negative regulation of signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Transcriptional Regulation by VENTX / replicative senescence / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / viral process / positive regulation of intrinsic apoptotic signaling pathway / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of fibroblast proliferation / general transcription initiation factor binding / positive regulation of execution phase of apoptosis / transcription repressor complex / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / response to gamma radiation / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / molecular function activator activity / transcription initiation-coupled chromatin remodeling / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / DNA damage response, signal transduction by p53 class mediator / TP53 Regulates Metabolic Genes / autophagy / TP53 Regulates Transcription of DNA Repair Genes / negative regulation of protein catabolic process / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / promoter-specific chromatin binding / Stabilization of p53 / molecular condensate scaffold activity / negative regulation of cell growth / cellular response to gamma radiation / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / PML body / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / PKR-mediated signaling
Similarity search - Function
MDM4 / : / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / 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 profile. / SWIB/MDM2 domain superfamily / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / Zn-finger in Ran binding protein and others / : / 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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / p53-like transcription factor, DNA-binding / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Protein Mdm4 / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsCheng, X.Y. / Zhang, B.L. / Li, Z.C. / Kuang, Z.K. / Su, Z.D.
CitationJournal: To Be Published
Title: The crystal structure of the N-terminal domain of MdmX in complex with p53p peptide fragment
Authors: Cheng, X.Y. / Zhang, B.L. / Li, Z.C. / Kuang, Z.K. / Su, Z.D.
History
DepositionApr 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular tumor antigen p53,Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2045
Polymers14,6271
Non-polymers5774
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area5890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.097, 65.097, 94.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

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


Mass: 14626.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P04637, UniProt: O15151
#2: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.44 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.16 / Details: 0.1 M MES pH 6.5, 2 M MgSO4 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.109→53.695 Å / Num. obs: 22483 / % possible obs: 100 % / Redundancy: 12.9 % / Net I/σ(I): 17

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.453
Highest resolutionLowest resolution
Rotation53.7 Å2.4 Å

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Processing

Software
NameVersionClassification
REFMACREFMAC5refinement
HKL-2000data collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C3Y

7c3y


Resolution: 2.11→53.7 Å / Cross valid method: NONE / ESU R: 0.142 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.225 490 5.009 %
Rwork0.224 --
obs-10599 96.9149 %
Displacement parametersBiso mean: 44.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.086 Å20 Å20 Å2
2--0.086 Å20 Å2
3----0.173 Å2
Refinement stepCycle: LAST / Resolution: 2.11→53.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 38 36 835

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