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- PDB-8bm5: Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reacti... -

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Basic information

Entry
Database: PDB / ID: 8bm5
TitleTernary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 7
Components
  • 14-3-3 protein sigma
  • Estrogen-related receptor gamma
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / dual-reactive compound
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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / 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-QQ0 / 14-3-3 protein sigma / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERR gamma Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach.
Authors: Somsen, B.A. / Schellekens, R.J.C. / Verhoef, C.J.A. / Arkin, M.R. / Ottmann, C. / Cossar, P.J. / Brunsveld, L.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1377
Polymers27,7692
Non-polymers3685
Water5,819323
1
A: 14-3-3 protein sigma
B: Estrogen-related receptor gamma
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,27414
Polymers55,5384
Non-polymers73510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5090 Å2
ΔGint-61 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.636, 111.994, 62.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

MG

21A-417-

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
Details: GAMGS at the beginning (-5 to -1) are part of the expression tag
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 / ERR gamma-2 / Estrogen receptor-related protein 3 / Nuclear receptor subfamily 3 group B member 3


Mass: 1215.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62508

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Non-polymers , 4 types, 328 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-QQ0 / 4-methanoyl-~{N}-methyl-~{N}-(2-sulfanylethyl)benzenesulfonamide


Mass: 259.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO3S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 53.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 5% 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 EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→45.59 Å / Num. obs: 57237 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 36.8
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 9.8 / Num. unique obs: 2766 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y1d

6y1d


Resolution: 1.4→45.59 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 5410 4.91 %
Rwork0.1655 --
obs0.1665 57217 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 19 323 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062043
X-RAY DIFFRACTIONf_angle_d0.9182770
X-RAY DIFFRACTIONf_dihedral_angle_d5.789305
X-RAY DIFFRACTIONf_chiral_restr0.077302
X-RAY DIFFRACTIONf_plane_restr0.009369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2411800.19453436X-RAY DIFFRACTION98
1.42-1.430.1891590.18713441X-RAY DIFFRACTION99
1.43-1.450.16972120.17533456X-RAY DIFFRACTION100
1.45-1.470.18121720.16783471X-RAY DIFFRACTION99
1.47-1.490.181560.16063492X-RAY DIFFRACTION99
1.49-1.510.17382310.16213463X-RAY DIFFRACTION99
1.51-1.530.20961670.16243540X-RAY DIFFRACTION100
1.53-1.550.18961680.16083449X-RAY DIFFRACTION100
1.55-1.580.17852270.16163492X-RAY DIFFRACTION100
1.58-1.60.18831850.1623488X-RAY DIFFRACTION100
1.6-1.630.19831610.16423478X-RAY DIFFRACTION100
1.63-1.660.2011890.16313509X-RAY DIFFRACTION100
1.66-1.690.18172030.17313484X-RAY DIFFRACTION100
1.69-1.730.17661730.17083526X-RAY DIFFRACTION100
1.73-1.760.17891600.1723481X-RAY DIFFRACTION100
1.76-1.810.19931730.17983503X-RAY DIFFRACTION100
1.81-1.850.18491720.16993530X-RAY DIFFRACTION100
1.85-1.90.21111850.16823496X-RAY DIFFRACTION100
1.9-1.960.18891890.16673496X-RAY DIFFRACTION100
1.96-2.020.19051890.16963475X-RAY DIFFRACTION100
2.02-2.090.18111880.15983503X-RAY DIFFRACTION100
2.09-2.180.16991510.16283568X-RAY DIFFRACTION100
2.18-2.270.17111800.15523457X-RAY DIFFRACTION99
2.27-2.390.20371660.15713514X-RAY DIFFRACTION100
2.39-2.540.14871650.16863516X-RAY DIFFRACTION100
2.54-2.740.15961780.17233503X-RAY DIFFRACTION100
2.74-3.020.2071650.17573497X-RAY DIFFRACTION100
3.02-3.450.19922020.16653476X-RAY DIFFRACTION100
3.45-4.350.18691900.14883486X-RAY DIFFRACTION99
4.35-45.590.191740.16983504X-RAY DIFFRACTION100

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