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- PDB-8c0l: FC-THF stabilizer of 14-3-3 and ERalpha -

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Basic information

Entry
Database: PDB / ID: 8c0l
TitleFC-THF stabilizer of 14-3-3 and ERalpha
Components
  • 14-3-3 protein sigma
  • ERalpha peptide
KeywordsSTRUCTURAL PROTEIN / 14-3-3 / stabilization / ERalpha / fusicoccin
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
Fusicoccin A-THF / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVisser, E.J. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Stabilization of the Estrogen receptor alpha - 14-3-3 interaction as a potential intervention strategy for endocrine resistance in breast cancer
Authors: Visser, E.J. / Donaldson Collier, M. / Siefert, J. / Konstantinidou, M. / Paul, S. / Cossar, P. / Miley, G. / Meijer, O. / Arkin, M.R. / Ottmann, C. / Zwart, W. / Brunsveld, L.
History
DepositionDec 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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)27,7353
Polymers27,1572
Non-polymers5791
Water5,026279
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)55,4706
Polymers54,3134
Non-polymers1,1572
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)81.880, 112.141, 62.707
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-FC7 / Fusicoccin A-THF / (1S,3aS,4R,5R,6R,7aS,10aS,10bR)-5-hydroxy-1-(methoxymethyl)-4,10b-dimethyl-7-(propan-2-yl)-1,2,3,3a,4,5,6,7a,8,9,10a,10b-dodecahydrocyclopenta[4',5']cycloocta[1',2':4,5]cyclopenta[1,2-b]furan-6-yl 4,6-O-(1-methylethylidene)-alpha-D-glucopyranoside


Mass: 578.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H50O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
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: Jun 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→66.13 Å / Num. obs: 38541 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.989 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1854 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→56.07 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 3778 5.12 %
Rwork0.1819 --
obs0.1832 38541 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→56.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 0 279 2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091964
X-RAY DIFFRACTIONf_angle_d1.0622655
X-RAY DIFFRACTIONf_dihedral_angle_d12.467358
X-RAY DIFFRACTIONf_chiral_restr0.053300
X-RAY DIFFRACTIONf_plane_restr0.01338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.32221600.31432514X-RAY DIFFRACTION97
1.62-1.640.29181220.27562598X-RAY DIFFRACTION100
1.64-1.660.32011330.2572585X-RAY DIFFRACTION100
1.66-1.690.22551250.26062628X-RAY DIFFRACTION100
1.69-1.710.29541550.24192576X-RAY DIFFRACTION100
1.71-1.740.2471340.21552646X-RAY DIFFRACTION100
1.74-1.770.22181300.22682559X-RAY DIFFRACTION100
1.77-1.80.27991540.20582587X-RAY DIFFRACTION100
1.8-1.830.22681430.20662580X-RAY DIFFRACTION100
1.83-1.860.24031200.19362597X-RAY DIFFRACTION100
1.86-1.90.24751450.1962626X-RAY DIFFRACTION100
1.9-1.940.24931670.2062562X-RAY DIFFRACTION100
1.94-1.990.21761230.2062632X-RAY DIFFRACTION100
1.99-2.040.24721340.21092602X-RAY DIFFRACTION100
2.04-2.090.18281310.18592573X-RAY DIFFRACTION100
2.09-2.160.2381440.16792583X-RAY DIFFRACTION100
2.16-2.230.17431450.16382604X-RAY DIFFRACTION100
2.23-2.310.1851670.16182565X-RAY DIFFRACTION100
2.31-2.40.20751480.16282597X-RAY DIFFRACTION100
2.4-2.510.21381700.15992542X-RAY DIFFRACTION100
2.51-2.640.21091280.16542602X-RAY DIFFRACTION100
2.64-2.80.18681260.18262603X-RAY DIFFRACTION100
2.8-3.020.19781520.17412612X-RAY DIFFRACTION100
3.02-3.320.20381250.16842602X-RAY DIFFRACTION100
3.32-3.810.16241250.16052590X-RAY DIFFRACTION100
3.81-4.790.20021260.1532615X-RAY DIFFRACTION100
4.8-56.070.17751460.19562608X-RAY DIFFRACTION100

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