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

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Basic information

Entry
Database: PDB / ID: 9fvh
TitleCrystal structure of 14-3-3 sigma in complex with Tau pS214 peptide and covalent stabilizer JS17
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 / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding ...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 / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / 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 / keratinocyte development / regulation of mitochondrial fission / 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 / dynactin binding / regulation of microtubule polymerization / cAMP/PKA signal transduction / apolipoprotein binding / Regulation of localization of FOXO transcription factors / main axon / keratinocyte proliferation / protein polymerization / axolemma / glial cell projection / phosphoserine residue binding / 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 mitochondrial fission / 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 / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of superoxide anion generation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / regulation of long-term synaptic depression / supramolecular fiber organization / 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 / protein export from nucleus / negative regulation of innate immune response / 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 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hsp90 protein binding / microglial cell activation / synapse organization / cellular response to nerve growth factor stimulus / protein homooligomerization / PKR-mediated signaling / 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: 1.45 Å
Authorsvan den Oetelaar, M.C.M. / Scheele, J.J.A. / 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. / Ottmann, C. / Cossar, P. / Brunsveld, L.
History
DepositionJun 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 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)28,4053
Polymers28,0632
Non-polymers3411
Water4,306239
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)56,8096
Polymers56,1274
Non-polymers6822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4270 Å2
ΔGint-33 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.100, 112.402, 62.433
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 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-A1IF5 / 2-bromanyl-4-[2-(2-methylphenyl)imidazol-1-yl]benzaldehyde


Mass: 341.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13BrN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
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: 0.873129 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873129 Å / Relative weight: 1
ReflectionResolution: 1.45→66.3 Å / Num. obs: 51458 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Net I/σ(I): 24.9
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 2506 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
REFMACREFMAC5refinement
Aimlessdata scaling
Cootmodel building
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→66.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.841 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17593 2645 5.1 %RANDOM
Rwork0.14726 ---
obs0.14873 48813 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.64 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.45→66.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 20 239 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0162004
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161906
X-RAY DIFFRACTIONr_angle_refined_deg1.381.8272713
X-RAY DIFFRACTIONr_angle_other_deg0.5631.5684406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6245.262267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg57.233204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6110373
X-RAY DIFFRACTIONr_chiral_restr0.0750.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_mcbond_it4.6311.741994
X-RAY DIFFRACTIONr_mcbond_other4.5911.74994
X-RAY DIFFRACTIONr_mcangle_it6.5733.1261253
X-RAY DIFFRACTIONr_mcangle_other6.5833.1311254
X-RAY DIFFRACTIONr_scbond_it7.4312.0961010
X-RAY DIFFRACTIONr_scbond_other7.4282.0961011
X-RAY DIFFRACTIONr_scangle_other10.4173.7061460
X-RAY DIFFRACTIONr_long_range_B_refined13.82922.492450
X-RAY DIFFRACTIONr_long_range_B_other12.70220.722391
X-RAY DIFFRACTIONr_rigid_bond_restr3.29133910
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 205 -
Rwork0.149 3555 -
obs--100 %

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