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- PDB-7ba9: Cys-42-tethered stabilizer 11 of 14-3-3(sigma)/ERa PPI -

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Basic information

Entry
Database: PDB / ID: 7ba9
TitleCys-42-tethered stabilizer 11 of 14-3-3(sigma)/ERa PPI
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsSIGNALING PROTEIN / protein-protein interaction / stabilizer / hub protein / transcription factor
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of epidermal cell division ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of epidermal cell division / protein kinase C inhibitor activity / epithelial cell proliferation involved in mammary gland duct elongation / positive regulation of epidermal cell differentiation / keratinocyte development / prostate epithelial cord elongation / keratinization / epithelial cell development / regulation of cell-cell adhesion / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / cAMP/PKA signal transduction / TFIIB-class transcription factor binding / Regulation of localization of FOXO transcription factors / steroid hormone receptor signaling pathway / androgen metabolic process / keratinocyte proliferation / phosphoserine residue binding / mammary gland alveolus development / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / cellular response to estrogen stimulus / estrogen response element binding / establishment of skin barrier / Mitochondrial unfolded protein response (UPRmt) / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / negative regulation of canonical NF-kappaB signal transduction / positive regulation of protein localization / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / protein sequestering activity / nitric-oxide synthase regulator activity / positive regulation of cell adhesion / negative regulation of innate immune response / protein export from nucleus / negative regulation of miRNA transcription / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of nitric-oxide synthase activity / ESR-mediated signaling / stem cell proliferation / transcription coregulator binding / positive regulation of protein export from nucleus / transcription corepressor binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / protein localization / PIP3 activates AKT signaling / response to estradiol / regulation of protein localization / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. ...14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 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 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-T6N / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsSijbesma, E. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.001.035 Netherlands
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Exploration of a 14-3-3 PPI Pocket by Covalent Fragments as Stabilizers.
Authors: Sijbesma, E. / Hallenbeck, K.K. / Andrei, S.A. / Rust, R.R. / Adriaans, J.M.C. / Brunsveld, L. / Arkin, M.R. / Ottmann, C.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 1.2Oct 23, 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

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7406
Polymers27,4142
Non-polymers3264
Water5,314295
1
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules

A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,48012
Polymers54,8284
Non-polymers6538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4320 Å2
ΔGint-40 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.736, 112.087, 62.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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.: 1
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 Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 870.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-T6N / 2-methyl-2-(4-methylphenoxy)-~{N}-(2-sulfanylethyl)propanamide


Mass: 253.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.095 M HEPES, 0.19 M CaCl2, 27% (v/v) PEG400, 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.48→66.04 Å / Num. obs: 47850 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.026 / Rrim(I) all: 0.094 / Net I/σ(I): 17.8 / Num. measured all: 624764 / Scaling rejects: 3
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
1.48-1.51131.7413031423290.6570.4921.811.699.6
8.11-66.04120.024422135110.0070.02575.399.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIXdev_3139refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.48→45.317 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 2330 4.87 %
Rwork0.18 45499 -
obs0.1815 47829 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.81 Å2 / Biso mean: 22.6345 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 1.48→45.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 20 295 2213
Biso mean--41.73 31.76 -
Num. residues----241
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.48-1.51020.26411300.2453262999
1.5102-1.54310.30381320.2415262599
1.5431-1.5790.30341470.2331263499
1.579-1.61850.26311200.2143264299
1.6185-1.66220.23691450.2022262999
1.6622-1.71110.25111330.19282640100
1.7111-1.76640.22981510.19782651100
1.7664-1.82950.21931370.18742665100
1.8295-1.90280.24281260.18192675100
1.9028-1.98930.19091430.17742656100
1.9893-2.09420.19311370.16222666100
2.0942-2.22540.19481480.172673100
2.2254-2.39730.1791300.16912712100
2.3973-2.63850.22241450.17492677100
2.6385-3.02020.23441220.1872739100
3.0202-3.80480.19371200.16852748100
3.8048-45.3170.19881640.17372838100

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