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- PDB-6v4h: Crystal Structure Analysis of Zebra Fish MDMX -

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Basic information

Entry
Database: PDB / ID: 6v4h
TitleCrystal Structure Analysis of Zebra Fish MDMX
Components
  • Protein Mdm4
  • Stapled Peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)
KeywordsAPOPTOSIS / p53 binding
Function / homology
Function and homology information


Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / 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 ...Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / 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 / positive regulation of programmed necrotic cell death / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / 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 / 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 / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / negative regulation of mitophagy / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / 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 / 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 / rRNA transcription / negative regulation of reactive oxygen species metabolic process / Transcriptional Regulation by VENTX / cellular response to UV-C / replicative senescence / general transcription initiation factor binding / cellular response to actinomycin D / 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 / positive regulation of execution phase of apoptosis / viral process / Pyroptosis / hematopoietic stem cell differentiation / response to X-ray / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / glial cell proliferation / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / mitophagy / cis-regulatory region sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / response to salt stress / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / negative regulation of proteolysis
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 ...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 superfamily / Zinc finger RanBP2-type signature. / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2020
Title: Identification of a Structural Determinant for Selective Targeting of HDMX.
Authors: Ben-Nun, Y. / Seo, H.S. / Harvey, E.P. / Hauseman, Z.J. / Wales, T.E. / Newman, C.E. / Cathcart, A.M. / Engen, J.R. / Dhe-Paganon, S. / Walensky, L.D.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 6, 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: Protein Mdm4
B: Stapled Peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)
C: Protein Mdm4
D: Stapled Peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)


Theoretical massNumber of molelcules
Total (without water)28,0604
Polymers28,0604
Non-polymers00
Water3,099172
1
A: Protein Mdm4
B: Stapled Peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)


Theoretical massNumber of molelcules
Total (without water)14,0302
Polymers14,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area5850 Å2
MethodPISA
2
C: Protein Mdm4
D: Stapled Peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)


Theoretical massNumber of molelcules
Total (without water)14,0302
Polymers14,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.220, 30.800, 68.850
Angle α, β, γ (deg.)90.000, 106.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11998.787 Da / Num. of mol.: 2 / Mutation: L46V, V95L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mdm4, mdmx / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZUW7
#2: Protein/peptide Stapled Peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)


Mass: 2031.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-8.0, 24% PEG 3350, 50mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→65.95 Å / Num. obs: 40591 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.233 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Net I/σ(I): 12.2 / Num. measured all: 137013
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1 / Num. measured all: 5514 / Num. unique obs: 1881 / Rpim(I) all: 0.714 / Rrim(I) all: 1.257 / % possible all: 92.1

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5T

4n5t


Resolution: 1.53→65.95 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.35
RfactorNum. reflection% reflection
Rfree0.1922 2009 4.95 %
Rwork0.158 --
obs0.1597 40578 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.62 Å2 / Biso mean: 33.3238 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: final / Resolution: 1.53→65.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 172 1859
Biso mean---44.27 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051770
X-RAY DIFFRACTIONf_angle_d0.8042397
X-RAY DIFFRACTIONf_dihedral_angle_d2.4371804
X-RAY DIFFRACTIONf_chiral_restr0.052265
X-RAY DIFFRACTIONf_plane_restr0.005307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.53-1.56830.31731350.2683260493
1.5683-1.61070.27671260.2369274798
1.6107-1.65810.25641330.2115272499
1.6581-1.71160.23561440.1819276799
1.7116-1.77280.22281370.1605276099
1.7728-1.84380.16251340.1495276299
1.8438-1.92770.19011640.1413269097
1.9277-2.02940.20161240.1476277699
2.0294-2.15650.18771380.1387276399
2.1565-2.3230.16061650.1406275899
2.323-2.55680.19551430.1509279698
2.5568-2.92680.19261650.1681273198
2.9268-3.68740.18271420.1562281999
3.6874-65.950.18941590.1559287298

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