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

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Basic information

Entry
Database: PDB / ID: 9gfa
TitleCrystal structure of 14-3-3 sigma in complex with Tau pS214 peptide and covalent stabilizer LD33
Components
  • 14-3-3 protein sigma
  • Microtubule-associated protein tau
KeywordsPEPTIDE BINDING PROTEIN / 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 / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / negative regulation of tubulin deacetylation ...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 / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / negative regulation of tubulin deacetylation / generation of neurons / regulation of epidermal cell division / protein kinase C inhibitor activity / rRNA metabolic process / axonal transport of mitochondrion / positive regulation of epidermal cell differentiation / regulation of mitochondrial fission / keratinocyte development / keratinization / axon development / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / regulation of cell-cell adhesion / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / regulation of microtubule polymerization / dynactin binding / cAMP/PKA signal transduction / apolipoprotein binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / main axon / protein polymerization / phosphoserine residue binding / glial cell projection / axolemma / negative regulation of mitochondrial fission / Activation of BAD and translocation to mitochondria / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of keratinocyte proliferation / regulation of microtubule polymerization or depolymerization / establishment of skin barrier / negative regulation of protein localization to plasma membrane / neurofibrillary tangle assembly / positive regulation of axon extension / 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 / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / positive regulation of superoxide anion generation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / synapse assembly / supramolecular fiber organization / RHO GTPases activate PKNs / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / regulation of calcium-mediated signaling / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / positive regulation of cell adhesion / nuclear periphery / regulation of microtubule cytoskeleton organization / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / cellular response to reactive oxygen species / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Hsp90 protein binding / microglial cell activation / synapse organization / PKR-mediated signaling / cellular response to nerve growth factor stimulus / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / response to lead ion / microtubule cytoskeleton organization / memory / 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
: / 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
Authorsvan den Oetelaar, M.C.M. / Engelen, S.F.H. / Ottmann, C. / Brunsveld, L.
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. / Engelen, S.F.H. / Cossar, P. / Ottmann, C. / Brunsveld, L.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 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)28,4443
Polymers28,0792
Non-polymers3641
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area12340 Å2
Unit cell
Length a, b, c (Å)82.384, 112.568, 62.459
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: 26558.914 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 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-A1IKN / 3-(3-bromanyl-4-methyl-phenyl)-2-pyridin-3-yl-1,2-dihydrobenzimidazole


Mass: 364.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14BrN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: ID30B / Wavelength: 0.885601 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885601 Å / Relative weight: 1
ReflectionResolution: 1.6→66.48 Å / Num. obs: 38694 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.999 / Net I/σ(I): 22.6
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1894 / CC1/2: 0.954

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5refinement
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→66.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.31 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19621 1974 5.1 %RANDOM
Rwork0.17349 ---
obs0.17466 36693 99.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-0 Å2
2---0.13 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→66.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 23 181 2074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0161933
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161836
X-RAY DIFFRACTIONr_angle_refined_deg1.571.8212603
X-RAY DIFFRACTIONr_angle_other_deg0.5871.5684241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275.28250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg52.95352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0510360
X-RAY DIFFRACTIONr_chiral_restr0.080.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_mcbond_it2.9921.86950
X-RAY DIFFRACTIONr_mcbond_other2.9851.859950
X-RAY DIFFRACTIONr_mcangle_it4.0373.3161184
X-RAY DIFFRACTIONr_mcangle_other4.0383.321185
X-RAY DIFFRACTIONr_scbond_it5.4942.342983
X-RAY DIFFRACTIONr_scbond_other5.492.342983
X-RAY DIFFRACTIONr_scangle_other7.3264.0571420
X-RAY DIFFRACTIONr_long_range_B_refined7.37122.332314
X-RAY DIFFRACTIONr_long_range_B_other7.35222.162284
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 150 -
Rwork0.174 2689 -
obs--100 %

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