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- PDB-8byf: fragment-linked stabilizer for ERa - 14-3-3 interaction (1047455) -

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Basic information

Entry
Database: PDB / ID: 8byf
Titlefragment-linked stabilizer for ERa - 14-3-3 interaction (1047455)
Components
  • 14-3-3 protein sigma
  • PHE-PRO-ALA-TPO-VAL
KeywordsSTRUCTURAL PROTEIN / 14-3-3 / ERa / fragment linking / stabilization
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 cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / 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 cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / 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-S6X / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 12, 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

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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: PHE-PRO-ALA-TPO-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5703
Polymers27,1572
Non-polymers4141
Water6,467359
1
A: 14-3-3 protein sigma
B: PHE-PRO-ALA-TPO-VAL
hetero molecules

A: 14-3-3 protein sigma
B: PHE-PRO-ALA-TPO-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1416
Polymers54,3134
Non-polymers8282
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3870 Å2
ΔGint-23 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.787, 112.194, 62.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26542.914 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 PHE-PRO-ALA-TPO-VAL


Mass: 613.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-S6X / ~{N}-[3-(5-carbamimidoylthiophen-3-yl)phenyl]-2-(4-chloranylphenoxy)-2-methyl-propanamide


Mass: 413.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.32 %
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: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.65→66.09 Å / Num. obs: 33440 / % possible obs: 95.8 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 14.4
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1045 / CC1/2: 0.615

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
DIALSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→34.2 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 1633 4.89 %
Rwork0.1686 --
obs0.1703 33413 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 28 359 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011982
X-RAY DIFFRACTIONf_angle_d1.032678
X-RAY DIFFRACTIONf_dihedral_angle_d5.431299
X-RAY DIFFRACTIONf_chiral_restr0.051290
X-RAY DIFFRACTIONf_plane_restr0.008371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.2808960.24071827X-RAY DIFFRACTION67
1.7-1.750.25061150.23252327X-RAY DIFFRACTION86
1.75-1.820.24161350.20112631X-RAY DIFFRACTION97
1.82-1.890.27541220.18752763X-RAY DIFFRACTION100
1.89-1.970.18461620.17622724X-RAY DIFFRACTION100
1.97-2.080.2371420.15182732X-RAY DIFFRACTION100
2.08-2.210.17471480.14682733X-RAY DIFFRACTION100
2.21-2.380.17191250.14192783X-RAY DIFFRACTION100
2.38-2.620.20661370.1552776X-RAY DIFFRACTION100
2.62-30.17931400.16442776X-RAY DIFFRACTION100
3-3.780.20081460.15682802X-RAY DIFFRACTION100
3.78-34.20.19231650.1822906X-RAY DIFFRACTION100

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