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- PDB-8byz: fragment-linked stabilizer for ERa - 14-3-3 interaction (AZ210) -

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Basic information

Entry
Database: PDB / ID: 8byz
Titlefragment-linked stabilizer for ERa - 14-3-3 interaction (AZ210)
Components
  • 14-3-3 protein sigma
  • ERalpha peptide
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 / Activation of BAD and translocation to mitochondria ...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 / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / 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 / protein kinase A signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / 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 / 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-SD7 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 14, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: ERalpha peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4835
Polymers27,1572
Non-polymers3263
Water5,729318
1
A: 14-3-3 protein sigma
B: ERalpha peptide
hetero molecules

A: 14-3-3 protein sigma
B: ERalpha peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,96510
Polymers54,3134
Non-polymers6526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3980 Å2
ΔGint-33 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.632, 111.805, 62.489
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 ERalpha peptide


Mass: 613.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SD7 / 4-[(2~{S})-3-azanyl-2-methyl-propyl]-7-methoxy-1-benzothiophene-2-carboximidamide


Mass: 277.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.15 %
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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→65.93 Å / Num. obs: 52501 / % possible obs: 93.1 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 17
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 1590 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→45.35 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1824 2540 4.84 %
Rwork0.1692 --
obs0.1698 52490 92.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 21 318 2230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091961
X-RAY DIFFRACTIONf_angle_d0.9352647
X-RAY DIFFRACTIONf_dihedral_angle_d6.447288
X-RAY DIFFRACTIONf_chiral_restr0.063289
X-RAY DIFFRACTIONf_plane_restr0.008359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.27191000.23641694X-RAY DIFFRACTION58
1.43-1.460.22991020.21861999X-RAY DIFFRACTION67
1.46-1.490.24181250.18742406X-RAY DIFFRACTION82
1.49-1.520.19751230.17712833X-RAY DIFFRACTION95
1.52-1.560.18151490.16892854X-RAY DIFFRACTION96
1.56-1.60.19151520.16272837X-RAY DIFFRACTION96
1.6-1.650.18261410.16322869X-RAY DIFFRACTION97
1.65-1.70.1811250.16652874X-RAY DIFFRACTION97
1.7-1.760.19851560.17382885X-RAY DIFFRACTION97
1.76-1.830.19571350.17632899X-RAY DIFFRACTION97
1.83-1.920.19621360.17352906X-RAY DIFFRACTION98
1.92-2.020.17761420.16282926X-RAY DIFFRACTION97
2.02-2.150.15091490.15162921X-RAY DIFFRACTION98
2.15-2.310.14851860.15052906X-RAY DIFFRACTION98
2.31-2.540.15981470.15062973X-RAY DIFFRACTION99
2.54-2.910.18941450.16633009X-RAY DIFFRACTION99
2.91-3.670.19111670.16773015X-RAY DIFFRACTION99
3.67-45.350.19041600.18633144X-RAY DIFFRACTION99

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