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- PDB-7ba8: Cys-42-tethered stabilizer 10 of 14-3-3(sigma)/ERa PPI -

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Basic information

Entry
Database: PDB / ID: 7ba8
TitleCys-42-tethered stabilizer 10 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 / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / epithelial cell proliferation involved in mammary gland duct elongation / keratinocyte development / epithelial cell development / keratinization / prostate epithelial cord elongation / regulation of cell-cell adhesion / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / Regulation of localization of FOXO transcription factors / steroid hormone receptor signaling pathway / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / cellular response to estrogen stimulus / establishment of skin barrier / negative regulation of protein localization to plasma membrane / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of stem cell proliferation / negative regulation of canonical NF-kappaB signal transduction / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / positive regulation of protein localization / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / protein kinase A signaling / steroid binding / protein sequestering activity / nitric-oxide synthase regulator activity / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / ESR-mediated signaling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of protein export from nucleus / positive regulation of nitric-oxide synthase activity / stem cell proliferation / cellular response to estradiol stimulus / transcription coregulator binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / stem cell differentiation / nuclear estrogen receptor binding / TP53 Regulates Metabolic Genes / positive regulation of DNA-binding transcription factor activity / negative regulation of protein kinase activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / protein localization / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / regulation of protein localization / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / positive regulation of cell growth
Similarity search - Function
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. ...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 / Zinc finger, C4 type (two domains) / 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
Similarity search - Domain/homology
Chem-T6H / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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)27,6774
Polymers27,4142
Non-polymers2642
Water4,954275
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)55,3558
Polymers54,8284
Non-polymers5274
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3940 Å2
ΔGint-21 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.702, 112.163, 62.269
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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-T6H / 2-methyl-2-phenoxy-~{N}-(2-sulfanylethyl)propanamide


Mass: 239.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 52.73 %
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: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.2→66.04 Å / Num. obs: 89026 / % possible obs: 99.6 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 18.2 / Num. measured all: 1064974
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
1.2-1.225.31.1592251142450.5350.5361.2881.494.3
6.46-66.0412.80.04183936550.9990.0110.04261.299.9

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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: 1.2→45.305 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 4482 5.04 %
Rwork0.1854 84507 -
obs0.1864 88989 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.29 Å2 / Biso mean: 18.8457 Å2 / Biso min: 9.58 Å2
Refinement stepCycle: final / Resolution: 1.2→45.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 17 275 2190
Biso mean--26.73 27.79 -
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 (%)
1.2-1.21360.3521410.318257693
1.2136-1.22790.28861630.2869268297
1.2279-1.24290.26331540.261277999
1.2429-1.25860.26871590.2442812100
1.2586-1.27520.21351490.23522767100
1.2752-1.29270.24081430.222812100
1.2927-1.31110.20161490.21092816100
1.3111-1.33070.22061360.2092812100
1.3307-1.35150.20771410.20252812100
1.3515-1.37370.19511350.2032803100
1.3737-1.39730.21631520.22791100
1.3973-1.42280.21971410.20482826100
1.4228-1.45010.22341480.19072805100
1.4501-1.47970.21761500.17862842100
1.4797-1.51190.1911540.16942794100
1.5119-1.54710.20891660.17132799100
1.5471-1.58580.19051580.1682806100
1.5858-1.62860.19741390.16732818100
1.6286-1.67660.18211700.16742796100
1.6766-1.73070.17751210.17242884100
1.7307-1.79250.23011470.1812812100
1.7925-1.86430.17751510.18522829100
1.8643-1.94920.22891430.18312839100
1.9492-2.05190.20751590.17742820100
2.0519-2.18050.17921640.16822833100
2.1805-2.34880.20151440.17162854100
2.3488-2.58520.22261620.17832875100
2.5852-2.95920.21091460.19542863100
2.9592-3.7280.19281650.1792904100
3.728-45.3050.20561320.1853046100

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