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- PDB-8b5p: Ternary structure of 14-3-3s, ERRg phosphopeptide and dual-reacti... -

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Basic information

Entry
Database: PDB / ID: 8b5p
TitleTernary structure of 14-3-3s, ERRg phosphopeptide and dual-reactive compound 10
Components
  • 14-3-3 protein sigma
  • Estrogen Related Receptor gamma phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / dual-reactive compound
Function / homology
Function and homology information


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 ...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 / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 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 / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
Similarity search - Domain/homology
Chem-OQ3 / 14-3-3 protein sigma
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
DepositionSep 23, 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

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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)28,1556
Polymers27,7692
Non-polymers3864
Water6,269348
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)56,31112
Polymers55,5384
Non-polymers7738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5130 Å2
ΔGint-61 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.470, 111.844, 62.521
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-404-

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 phosphopeptide


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

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Non-polymers , 4 types, 352 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-OQ3 / 3-bromanyl-5-methanoyl-~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide


Mass: 302.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12BrNO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
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→45.51 Å / Num. obs: 56735 / % possible obs: 99.5 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 33.6
Reflection shellResolution: 1.4→1.43 Å / Mean I/σ(I) obs: 7.7 / Num. unique obs: 2790 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y1d

6y1d


Resolution: 1.4→45.51 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 5474 5.02 %
Rwork0.1704 103659 -
obs0.1711 56711 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.5 Å2 / Biso mean: 14.9469 Å2 / Biso min: 2.72 Å2
Refinement stepCycle: final / Resolution: 1.4→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 18 348 2264
Biso mean--13.8 25.37 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.27971970.23933353355096
1.42-1.430.20041650.20883359352498
1.43-1.450.21442140.19433420363498
1.45-1.470.19831450.18043381352698
1.47-1.490.16191780.17293490366899
1.49-1.510.18591770.1743448362599
1.51-1.530.18391790.17723397357699
1.53-1.550.21941770.17413432360999
1.55-1.580.18341740.172135003674100
1.58-1.60.17571890.16663432362199
1.6-1.630.18481890.17233419360899
1.63-1.660.19531630.165635463709100
1.66-1.690.18041710.169834843655100
1.69-1.730.19161620.171534733635100
1.73-1.760.18551900.185534863676100
1.77-1.810.20461910.185434323623100
1.81-1.850.17571820.177234803662100
1.85-1.90.16861950.175434573652100
1.9-1.960.18991920.169234703662100
1.96-2.020.19232060.172234663672100
2.02-2.090.17872080.155634503658100
2.09-2.180.16251850.159635083693100
2.18-2.280.1921730.16023438361199
2.28-2.40.18391690.160935023671100
2.4-2.550.17881710.171134533624100
2.55-2.740.20822030.177134843687100
2.74-3.020.16811660.174135083674100
3.02-3.450.19671960.169834733669100
3.45-4.350.15991740.15463454362899
4.35-45.510.18571930.172634643657100

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