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- PDB-8bzb: co-soak stabilizers for ERa - 14-3-3 interaction (884_AZ275) -

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Basic information

Entry
Database: PDB / ID: 8bzb
Titleco-soak stabilizers for ERa - 14-3-3 interaction (884_AZ275)
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsSTRUCTURAL PROTEIN / 14-3-3 / ERa / fragment linking / stabilization
Function / homology
Function and homology information


steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / Developmental Lineage of Mammary Gland Alveolar Cells / regulation of cell-cell adhesion / TFIIB-class transcription factor binding ...steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / Developmental Lineage of Mammary Gland Alveolar Cells / regulation of cell-cell adhesion / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / establishment of skin barrier / Regulation of localization of FOXO transcription factors / nuclear receptor-mediated steroid hormone signaling pathway / Regulation of GBP-mediated host defense / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Mitochondrial unfolded protein response (UPRmt) / negative regulation of protein localization to plasma membrane / Nuclear signaling by ERBB4 / cAMP/PKA signal transduction / protein export from nucleus / estrogen receptor signaling pathway / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / RNA polymerase II preinitiation complex assembly / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of nitric-oxide synthase activity / steroid binding / positive regulation of protein localization / stem cell differentiation / positive regulation of protein export from nucleus / protein localization to chromatin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 14-3-3 protein binding / ESR-mediated signaling / negative regulation of miRNA transcription / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / TBP-class protein binding / nuclear estrogen receptor binding / nitric-oxide synthase regulator activity / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / transcription coregulator binding / cellular response to estradiol stimulus / TP53 Regulates Metabolic Genes / SUMOylation of intracellular receptors / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / euchromatin / protein sequestering activity / Nuclear Receptor transcription pathway / response to estrogen / beta-catenin binding / nuclear receptor activity / transcription coactivator binding / intracellular protein localization / positive regulation of nitric oxide biosynthetic process / Constitutive Signaling by Aberrant PI3K in Cancer / sequence-specific double-stranded DNA binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / regulation of protein localization / PIP3 activates AKT signaling / positive regulation of cell growth / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / Golgi apparatus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. ...14-3-3 domain / Delta-Endotoxin; domain 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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-GEH / 4-ethoxy-1-benzothiophene-2-carboximidamide / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVisser, E.J. / Sijbesma, E. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking.
Authors: Visser, E.J. / Jaishankar, P. / Sijbesma, E. / Pennings, M.A.M. / Vandenboorn, E.M.F. / Guillory, X. / Neitz, R.J. / Morrow, J. / Dutta, S. / Renslo, A.R. / Brunsveld, L. / Arkin, M.R. / Ottmann, C.
History
DepositionDec 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 30, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Sep 13, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Sep 25, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Nov 13, 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: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7137
Polymers27,1462
Non-polymers5675
Water5,567309
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)55,42514
Polymers54,2914
Non-polymers1,13410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)81.905, 112.491, 62.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 26531.955 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: 613.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372

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Non-polymers , 4 types, 314 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 273.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16ClNO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SDM / 4-ethoxy-1-benzothiophene-2-carboximidamide


Mass: 220.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES (pH 7.1), PEG400 (24% (v/v)), 0.19 M CaCl2 and 5% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.7→66.21 Å / Num. obs: 31123 / % possible obs: 97 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 28.7
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1174 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.95 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 1570 5.05 %
Rwork0.1634 --
obs0.1649 31097 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 35 309 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091980
X-RAY DIFFRACTIONf_angle_d1.0362674
X-RAY DIFFRACTIONf_dihedral_angle_d6.508299
X-RAY DIFFRACTIONf_chiral_restr0.05290
X-RAY DIFFRACTIONf_plane_restr0.007370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.22081040.17212052X-RAY DIFFRACTION76
1.75-1.820.21211230.1652505X-RAY DIFFRACTION92
1.82-1.890.23021510.16512718X-RAY DIFFRACTION99
1.89-1.980.24051510.16412742X-RAY DIFFRACTION100
1.98-2.080.19191500.15192742X-RAY DIFFRACTION100
2.08-2.210.20631490.14532732X-RAY DIFFRACTION100
2.21-2.380.16161310.1472777X-RAY DIFFRACTION100
2.38-2.620.17441580.15742763X-RAY DIFFRACTION100
2.62-30.18321550.17242768X-RAY DIFFRACTION100
3-3.780.1711360.16052815X-RAY DIFFRACTION100
3.78-40.950.20741620.18322913X-RAY DIFFRACTION100

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