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- PDB-8bza: single soak stabilizer for ERa - 14-3-3 interaction (AZ555) -

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Basic information

Entry
Database: PDB / ID: 8bza
Titlesingle soak stabilizer for ERa - 14-3-3 interaction (AZ555)
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 / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue 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 / cAMP/PKA signal transduction / 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 / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular 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 domain / Delta-Endotoxin; domain 1 / 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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-methyl-5-phenyl-thiophene-2-carboximidamide / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 1.4Nov 13, 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)27,4466
Polymers27,1572
Non-polymers2894
Water5,098283
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)54,89112
Polymers54,3134
Non-polymers5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)81.842, 111.897, 62.456
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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-L1T / 4-methyl-5-phenyl-thiophene-2-carboximidamide


Mass: 216.302 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H12N2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 53.28 %
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: 1.25→66.06 Å / Num. obs: 79212 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 6.4
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 3858 / CC1/2: 0.442

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→55.95 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 3935 4.97 %
Rwork0.1827 --
obs0.1834 79184 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 18 283 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081965
X-RAY DIFFRACTIONf_angle_d0.9872652
X-RAY DIFFRACTIONf_dihedral_angle_d6.444276
X-RAY DIFFRACTIONf_chiral_restr0.069289
X-RAY DIFFRACTIONf_plane_restr0.009346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.29331380.30882634X-RAY DIFFRACTION100
1.27-1.280.29261400.29812668X-RAY DIFFRACTION99
1.28-1.30.3411470.28552639X-RAY DIFFRACTION100
1.3-1.320.31761350.27712651X-RAY DIFFRACTION99
1.32-1.330.29741320.26282668X-RAY DIFFRACTION99
1.33-1.350.29241330.25972643X-RAY DIFFRACTION100
1.35-1.380.28361430.25652650X-RAY DIFFRACTION100
1.38-1.40.34261310.27432668X-RAY DIFFRACTION100
1.4-1.420.25741420.26482665X-RAY DIFFRACTION100
1.42-1.450.23671460.22822681X-RAY DIFFRACTION100
1.45-1.480.22021640.20042625X-RAY DIFFRACTION100
1.48-1.510.20211250.18652705X-RAY DIFFRACTION100
1.51-1.540.23691400.19082652X-RAY DIFFRACTION100
1.54-1.570.17991290.1772688X-RAY DIFFRACTION100
1.57-1.610.18661350.16782684X-RAY DIFFRACTION100
1.61-1.660.19971300.16842683X-RAY DIFFRACTION100
1.66-1.710.20951500.17352678X-RAY DIFFRACTION100
1.71-1.760.2341330.17922693X-RAY DIFFRACTION100
1.76-1.820.17911430.1792698X-RAY DIFFRACTION100
1.82-1.90.1711290.17322697X-RAY DIFFRACTION100
1.9-1.980.18871430.16652706X-RAY DIFFRACTION100
1.98-2.090.16031490.1592679X-RAY DIFFRACTION100
2.09-2.220.16321330.15572721X-RAY DIFFRACTION100
2.22-2.390.17091470.14862717X-RAY DIFFRACTION100
2.39-2.630.15151410.15912696X-RAY DIFFRACTION100
2.63-3.010.1831470.17612751X-RAY DIFFRACTION100
3.01-3.790.18321490.17612747X-RAY DIFFRACTION100
3.8-55.950.20561610.192862X-RAY DIFFRACTION100

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