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- PDB-6yr5: 14-3-3 sigma in complex with hDMX-367 peptide -

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Basic information

Entry
Database: PDB / ID: 6yr5
Title14-3-3 sigma in complex with hDMX-367 peptide
Components
  • 14-3-3 protein sigma
  • Protein Mdm4
KeywordsPEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / DNA damage response, signal transduction by p53 class mediator / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / transcription repressor complex / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Stabilization of p53 / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / negative regulation of protein catabolic process / ubiquitin-protein transferase activity / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of TP53 Degradation / cellular response to hypoxia / positive regulation of cell growth / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / cadherin binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MDM4 / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily ...MDM4 / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / 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 / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Protein Mdm4 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWolter, M. / Srdanovic, S. / Ottman, C. / Warriner, S. / Wilson, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission675179European Union
CitationJournal: Febs J. / Year: 2022
Title: Understanding the interaction of 14-3-3 proteins with hDMX and hDM2: a structural and biophysical study.
Authors: Srdanovic, S. / Wolter, M. / Trinh, C.H. / Ottmann, C. / Warriner, S.L. / Wilson, A.J.
History
DepositionApr 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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
A: 14-3-3 protein sigma
O: Protein Mdm4
B: 14-3-3 protein sigma
P: Protein Mdm4
C: 14-3-3 protein sigma
Q: Protein Mdm4
D: 14-3-3 protein sigma
R: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9959
Polymers112,8998
Non-polymers961
Water6,684371
1
A: 14-3-3 protein sigma
O: Protein Mdm4
B: 14-3-3 protein sigma
P: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5465
Polymers56,4504
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-40 kcal/mol
Surface area22770 Å2
MethodPISA
2
C: 14-3-3 protein sigma
Q: Protein Mdm4

D: 14-3-3 protein sigma
R: Protein Mdm4


Theoretical massNumber of molelcules
Total (without water)56,4504
Polymers56,4504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3930 Å2
ΔGint-30 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.950, 75.300, 78.390
Angle α, β, γ (deg.)95.150, 113.140, 93.840
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide
Protein Mdm4 / Double minute 4 protein / Mdm2-like p53-binding protein / Protein Mdmx / p53-binding protein Mdm4


Mass: 1681.894 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-Tris propane pH 7, 0.2 M Sodium citrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033208 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033208 Å / Relative weight: 1
ReflectionResolution: 2.1→74.53 Å / Num. obs: 75667 / % possible obs: 97.4 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.051 / Rrim(I) all: 0.125 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.145.90.6732650844740.7970.2980.7392.896.4
10.5-71.56.80.08141276070.980.0350.08821.498.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
PHENIX1.12refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DAT

4dat


Resolution: 2.25→74.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.156 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.186
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 2993 4.9 %RANDOM
Rwork0.1975 ---
obs0.1987 58664 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.17 Å2 / Biso mean: 31.365 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-0.27 Å20.1 Å2
2---1.32 Å2-0.1 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.25→74.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7324 0 5 371 7700
Biso mean--65.07 34.67 -
Num. residues----943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137439
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176973
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.64310034
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5816140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22822.248387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74151343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.741555
X-RAY DIFFRACTIONr_chiral_restr0.0820.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 206 -
Rwork0.295 4295 -
all-4501 -
obs--96.32 %

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