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- PDB-6xy5: Ternary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor... -

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Basic information

Entry
Database: PDB / ID: 6xy5
TitleTernary complex of 14-3-3 sigma (C38N), Estrogen Related Receptor gamma (DBD) phosphopeptide, and disulfide PPI stabilizer 5
Components
  • 14-3-3 protein sigma
  • Estrogen Related Receptor gamma phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / ERRy phosphopeptide / disulfide / stabilization
Function / homology
Function and homology information


AF-2 domain binding / nuclear steroid receptor activity / 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 / phosphoserine residue binding ...AF-2 domain binding / nuclear steroid receptor activity / 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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / retinoic acid receptor signaling pathway / establishment of skin barrier / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / intracellular steroid hormone receptor signaling pathway / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / steroid binding / 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 / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Nuclear Receptor transcription pathway / nuclear receptor activity / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / 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 / cytosol / cytoplasm
Similarity search - Function
Oestrogen-related receptor / Retinoic acid 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 ...Oestrogen-related receptor / Retinoic acid 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 / 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-O4E / 14-3-3 protein sigma / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionJan 29, 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

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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 Related Receptor gamma phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1296
Polymers27,7712
Non-polymers3584
Water6,864381
1
A: 14-3-3 protein sigma
B: Estrogen Related Receptor gamma phosphopeptide
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,25912
Polymers55,5424
Non-polymers7168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5390 Å2
ΔGint-57 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.302, 112.109, 62.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 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 phosphopeptide


Mass: 1217.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62508*PLUS

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Non-polymers , 4 types, 385 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-O4E / 3-bromanyl-~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide


Mass: 274.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12BrNOS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 52.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.3→66.34 Å / Num. obs: 71045 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3575 / CC1/2: 0.912

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Processing

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

3p1n


Resolution: 1.3→56.054 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.33
RfactorNum. reflection% reflection
Rfree0.1775 6924 5.05 %
Rwork0.1621 --
obs0.1628 71009 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.57 Å2 / Biso mean: 15.8466 Å2 / Biso min: 5.81 Å2
Refinement stepCycle: final / Resolution: 1.3→56.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 17 381 2284
Biso mean--35.19 26.87 -
Num. residues----242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.3-1.31480.25612140.2202X-RAY DIFFRACTION099
1.3148-1.33020.21372480.2139X-RAY DIFFRACTION098
1.3302-1.34650.20162300.2088X-RAY DIFFRACTION0100
1.3465-1.36350.23222280.2034X-RAY DIFFRACTION098
1.3635-1.38150.2112270.2082X-RAY DIFFRACTION099
1.3815-1.40040.19912240.2039X-RAY DIFFRACTION099
1.4004-1.42040.20342350.1996X-RAY DIFFRACTION099
1.4204-1.44160.22022420.1904X-RAY DIFFRACTION0100
1.4416-1.46410.20642470.1787X-RAY DIFFRACTION099
1.4641-1.48810.2092350.1763X-RAY DIFFRACTION099
1.4881-1.51380.17762300.1697X-RAY DIFFRACTION0100
1.5138-1.54130.20812360.1722X-RAY DIFFRACTION099
1.5413-1.5710.21171980.1625X-RAY DIFFRACTION0100
1.571-1.6030.16622370.1612X-RAY DIFFRACTION0100
1.603-1.63790.16622390.1574X-RAY DIFFRACTION0100
1.6379-1.6760.16532210.159X-RAY DIFFRACTION0100
1.676-1.71790.17552200.1523X-RAY DIFFRACTION0100
1.7179-1.76440.19112070.1613X-RAY DIFFRACTION0100
1.7644-1.81630.17022670.1616X-RAY DIFFRACTION0100
1.8163-1.87490.18552530.1627X-RAY DIFFRACTION0100
1.8749-1.94190.20612520.1571X-RAY DIFFRACTION0100
1.9419-2.01970.17852530.1539X-RAY DIFFRACTION0100
2.0197-2.11160.13852240.1447X-RAY DIFFRACTION0100
2.1116-2.22290.16692210.144X-RAY DIFFRACTION0100
2.2229-2.36220.17142260.1359X-RAY DIFFRACTION0100
2.3622-2.54460.162010.1427X-RAY DIFFRACTION0100
2.5446-2.80070.14781960.1547X-RAY DIFFRACTION0100
2.8007-3.20590.15782310.1601X-RAY DIFFRACTION0100
3.2059-4.03890.17062500.1555X-RAY DIFFRACTION0100
4.0389-56.0540.18772320.1749X-RAY DIFFRACTION0100

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