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

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Basic information

Entry
Database: PDB / ID: 9gga
TitleCrystal structure of 14-3-3 sigma in complex with Tau pS214 peptide and covalent stabilizer FM089
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 / 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 / positive regulation of epidermal cell differentiation / axonal transport of mitochondrion / keratinocyte development / keratinization / regulation of mitochondrial fission / 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 / Regulation of localization of FOXO transcription factors / apolipoprotein binding / keratinocyte proliferation / main axon / protein polymerization / glial cell projection / axolemma / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of mitochondrial fission / negative regulation of keratinocyte proliferation / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / establishment of skin barrier / negative regulation of protein localization to plasma membrane / neurofibrillary tangle assembly / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of axon extension / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / synapse assembly / positive regulation of superoxide anion generation / RHO GTPases activate PKNs / supramolecular fiber organization / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to reactive oxygen species / 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: 2.24 Å
Authorsvan den Oetelaar, M.C.M. / Brunsveld, L. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Modulation of Tau Condensation with 14-3-3/Tau Molecular Glues
Authors: van den Oetelaar, M.C.M. / Ravatt, L. / Maqueda Zelaya, F. / Oberheide, A.O. / van de Wijngaart, T.R. / van Veldhuisen, T.W. / van Boxtel, F.M.A. / Verhoef, C.J.A. / Cossar, P.J. / Wegmann, ...Authors: van den Oetelaar, M.C.M. / Ravatt, L. / Maqueda Zelaya, F. / Oberheide, A.O. / van de Wijngaart, T.R. / van Veldhuisen, T.W. / van Boxtel, F.M.A. / Verhoef, C.J.A. / Cossar, P.J. / Wegmann, S. / Ottmann, C. / Brunsveld, L.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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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
P: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4763
Polymers28,0792
Non-polymers3961
Water1,08160
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)56,9526
Polymers56,1594
Non-polymers7932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4530 Å2
ΔGint-25 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.516, 112.340, 62.729
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-A1IKS / 2-bromanyl-4-[[(3~{R})-3-oxidanyl-3,4-dihydro-2~{H}-quinolin-1-yl]sulfonyl]benzaldehyde


Mass: 396.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14BrNO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
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: ID30B / Wavelength: 0.885601 Å
DetectorType: DECTRIS EIGER2 X 9M / 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: 2.24→66.5 Å / Num. obs: 72024 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.995 / Net I/σ(I): 18.5
Reflection shellResolution: 2.24→2.31 Å / Num. unique obs: 6515 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→56.17 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2606 10.05 %RANDOM
Rwork0.1939 ---
obs0.1944 25924 95.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→56.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 22 60 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131924
X-RAY DIFFRACTIONf_angle_d1.4272597
X-RAY DIFFRACTIONf_dihedral_angle_d15.52735
X-RAY DIFFRACTIONf_chiral_restr0.066286
X-RAY DIFFRACTIONf_plane_restr0.031335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.23281290.21321252X-RAY DIFFRACTION97
2.28-2.320.21551400.20371230X-RAY DIFFRACTION96
2.32-2.370.20471330.20461200X-RAY DIFFRACTION96
2.37-2.420.26761410.20821252X-RAY DIFFRACTION95
2.42-2.480.2341340.21661218X-RAY DIFFRACTION95
2.48-2.540.22931390.20381198X-RAY DIFFRACTION95
2.54-2.610.25741460.21791273X-RAY DIFFRACTION97
2.61-2.690.21871390.1981224X-RAY DIFFRACTION97
2.69-2.770.2111350.23791203X-RAY DIFFRACTION93
2.77-2.870.21761380.21371225X-RAY DIFFRACTION96
2.87-2.990.21851400.20671220X-RAY DIFFRACTION95
2.99-3.120.24221360.22361258X-RAY DIFFRACTION97
3.12-3.290.2251380.20591238X-RAY DIFFRACTION98
3.29-3.490.21091370.21274X-RAY DIFFRACTION97
3.5-3.760.17191320.18191231X-RAY DIFFRACTION96
3.77-4.140.1461340.16851208X-RAY DIFFRACTION95
4.14-4.740.15231410.15921212X-RAY DIFFRACTION95
4.74-5.970.18771430.18931223X-RAY DIFFRACTION96
5.98-56.170.18221310.16971179X-RAY DIFFRACTION91

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