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- PDB-6y3w: Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor... -

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Basic information

Entry
Database: PDB / ID: 6y3w
TitleTernary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD) phosphopeptide, and disulfide PPI stabilizer 1
Components
  • 14-3-3 protein sigma
  • Estrogen Related Receptor gamma phosphopetide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / ERRy phosphopeptide / disulfide / stabilization
Function / homology
Function and homology information


AF-2 domain binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / nuclear steroid receptor activity / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors ...AF-2 domain binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / nuclear steroid receptor activity / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / estrogen response element binding / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / establishment of skin barrier / 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 / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / retinoic acid receptor signaling pathway / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / steroid binding / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / 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 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Nuclear Receptor transcription pathway / nuclear receptor activity / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / intracellular protein localization / regulation of protein localization / positive regulation of cold-induced thermogenesis / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / cadherin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Oestrogen-related receptor / Retinoic acid receptor / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...Oestrogen-related receptor / Retinoic acid receptor / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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-O85 / 14-3-3 protein sigma / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.001.035 Netherlands
Netherlands Organisation for Scientific Research (NWO)016.150.366 Netherlands
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Fluorescence Anisotropy-Based Tethering for Discovery of Protein-Protein Interaction Stabilizers.
Authors: Sijbesma, E. / Somsen, B.A. / Miley, G.P. / Leijten-van de Gevel, I.A. / Brunsveld, L. / Arkin, M.R. / Ottmann, C.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_site_gen.auth_seq_id

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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 Related Receptor gamma phosphopetide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0917
Polymers27,7692
Non-polymers3225
Water6,593366
1
A: 14-3-3 protein sigma
B: Estrogen Related Receptor gamma phosphopetide
hetero molecules

A: 14-3-3 protein sigma
B: Estrogen Related Receptor gamma phosphopetide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,18214
Polymers55,5384
Non-polymers64310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5400 Å2
ΔGint-57 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.532, 112.487, 62.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

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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: 26553.875 Da / Num. of mol.: 1 / Mutation: C38N
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 Related Receptor gamma phosphopetide


Mass: 1215.370 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide contains a C-terminal amide, whereby the nitrogen is build in as ligand
Source: (synth.) Homo sapiens (human) / References: UniProt: P62508*PLUS

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Non-polymers , 4 types, 371 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-O85 / 3-fluoranyl-~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide


Mass: 213.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12FNOS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES (pH 7.3), 0.19 M CaCl2, 25% (v/v) PEG 400 and 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.34→66.54 Å / Num. obs: 65188 / % possible obs: 99.2 % / Redundancy: 11.4 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.34→1.36 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2959 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P1N

3p1n


Resolution: 1.34→45.646 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1866 1680 2.58 %
Rwork0.1637 63477 -
obs0.1643 65157 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.82 Å2 / Biso mean: 19.1733 Å2 / Biso min: 6.8 Å2
Refinement stepCycle: final / Resolution: 1.34→45.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 30 366 2281
Biso mean--25.27 30.14 -
Num. residues----243
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.34-1.37940.29641340.2575480192
1.3794-1.4240.23541510.2308521699
1.424-1.47490.21431250.20215248100
1.4749-1.53390.20671440.17965296100
1.5339-1.60370.20211350.16685290100
1.6037-1.68830.17171260.15445312100
1.6883-1.79410.1551510.15745329100
1.7941-1.93260.18831400.1615289100
1.9326-2.12710.19091350.15345364100
2.1271-2.43480.16191420.14625358100
2.4348-3.06760.19281520.15875389100
3.0676-45.6460.1831450.16395585100

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