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- PDB-9fs4: Crystal structure of 14-3-3 sigma in complex with Tau pS214 pepti... -

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Basic information

Entry
Database: PDB / ID: 9fs4
TitleCrystal structure of 14-3-3 sigma in complex with Tau pS214 peptide and covalent stabilizer LD12
Components
  • 14-3-3 protein sigma
  • Microtubule-associated protein tau
KeywordsPROTEIN BINDING / 14-3-3 / tau / protein-protein interaction / covalent stabilization
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / generation of neurons / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / keratinization / regulation of mitochondrial fission / axon development / central nervous system neuron development / regulation of cell-cell adhesion / intracellular distribution of mitochondria / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / apolipoprotein binding / phosphoserine residue binding / axolemma / protein polymerization / glial cell projection / negative regulation of mitochondrial fission / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / neurofibrillary tangle assembly / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / synapse assembly / supramolecular fiber organization / positive regulation of protein localization / regulation of calcium-mediated signaling / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / axon cytoplasm / stress granule assembly / phosphatidylinositol binding / positive regulation of cell adhesion / regulation of microtubule cytoskeleton organization / nuclear periphery / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / positive regulation of superoxide anion generation / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / astrocyte activation / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to lead ion / synapse organization / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / intrinsic apoptotic signaling pathway in response to DNA damage / neuron projection development / intracellular protein localization / cell-cell signaling
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / 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
2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOetelaar, M.C.M. / Ottmann, C. / Brunsveld, L. / Engelen, S.F.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Site-selective stabilization of the 14-3-3/tau protein-protein interaction
Authors: Oberheide, A.O. / van den Oetelaar, M.C.M. / Scheele, J.J.A. / Ottmann, C. / Cossar, P. / Brunsveld, L. / Engelen, S.F.H.
History
DepositionJun 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3783
Polymers28,0502
Non-polymers3271
Water3,657203
1
A: 14-3-3 protein sigma
P: Microtubule-associated protein tau
hetero molecules

A: 14-3-3 protein sigma
P: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7556
Polymers56,1014
Non-polymers6542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4460 Å2
ΔGint-28 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.343, 112.226, 62.420
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: 26529.850 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 Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1520.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Chemical ChemComp-TJ8 / 2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / LvD1009


Mass: 327.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H11BrN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10mg/mL 14-3-3sigma delta C, 1.5eq peptide, 0.095 M HEPES pH 7.1, 28% PEG400, 0.19 M CaCl2, 5% (v/v) glycerol compound soaked

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972425 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972425 Å / Relative weight: 1
ReflectionResolution: 1.6→66.39 Å / Num. obs: 35088 / % possible obs: 91.1 % / Redundancy: 1.9 % / CC1/2: 1 / Net I/σ(I): 27.4
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1884 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
REFMACRefmac5refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→66.39 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.343 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19776 1794 5.1 %RANDOM
Rwork0.18172 ---
obs0.18256 33294 91.1 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å2-0 Å2
2---0.2 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→66.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 19 203 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0171924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161821
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.832585
X-RAY DIFFRACTIONr_angle_other_deg0.3821.5664210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5825.264246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.53252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26410355
X-RAY DIFFRACTIONr_chiral_restr0.0410.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
X-RAY DIFFRACTIONr_mcbond_it4.6952.239949
X-RAY DIFFRACTIONr_mcbond_other4.6442.239949
X-RAY DIFFRACTIONr_mcangle_it5.8333.9921175
X-RAY DIFFRACTIONr_mcangle_other5.8433.9981176
X-RAY DIFFRACTIONr_scbond_it7.9332.789975
X-RAY DIFFRACTIONr_scbond_other7.9312.789975
X-RAY DIFFRACTIONr_scangle_other9.644.8221411
X-RAY DIFFRACTIONr_long_range_B_refined9.87525.722318
X-RAY DIFFRACTIONr_long_range_B_other9.8825.042260
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 147 -
Rwork0.204 2680 -
obs--100 %

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