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- PDB-9qnk: Tau pT245 phosphopeptide binding to 14-3-3sigma -

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Basic information

Entry
Database: PDB / ID: 9qnk
TitleTau pT245 phosphopeptide binding to 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • Microtubule-associated protein tau
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 protein-protein interactions
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 / Regulation of localization of FOXO transcription factors / apolipoprotein binding / main axon / keratinocyte proliferation / protein polymerization / axolemma / glial cell projection / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of keratinocyte proliferation / establishment of skin barrier / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / 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 / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / positive regulation of cell adhesion / nuclear periphery / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / regulation of microtubule cytoskeleton organization / 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 / cellular response to nerve growth factor stimulus / protein homooligomerization / synapse organization / regulation of synaptic plasticity / PKR-mediated signaling / response to lead ion / SH3 domain binding / 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
AuthorsPennings, M.A.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101077879European Union
CitationJournal: Digit Discov / Year: 2025
Title: Identifying 14-3-3 interactome binding sites with deep learning.
Authors: van Weesep, L. / Ozcelik, R. / Pennings, M. / Criscuolo, E. / Ottmann, C. / Brunsveld, L. / Grisoni, F.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)27,7326
Polymers27,5922
Non-polymers1404
Water3,315184
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)55,46412
Polymers55,1844
Non-polymers2808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5330 Å2
ΔGint-88 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.915, 113.043, 63.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

CA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#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: 1049.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636

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Non-polymers , 4 types, 188 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.6→45.96 Å / Num. obs: 34194 / % possible obs: 86.5 % / Redundancy: 12.3 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1931 / CC1/2: 0.777

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Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.022 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19581 1739 5.1 %RANDOM
Rwork0.16801 ---
obs0.16939 32431 86.52 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0 Å2
2---0.12 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 4 184 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0161993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161895
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.8252693
X-RAY DIFFRACTIONr_angle_other_deg0.5241.5674386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3425.26269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46510377
X-RAY DIFFRACTIONr_chiral_restr0.0680.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_mcbond_it11.0871.821993
X-RAY DIFFRACTIONr_mcbond_other10.6681.821993
X-RAY DIFFRACTIONr_mcangle_it9.7423.2231242
X-RAY DIFFRACTIONr_mcangle_other9.7593.2251243
X-RAY DIFFRACTIONr_scbond_it15.5152.3211000
X-RAY DIFFRACTIONr_scbond_other14.8122.3171000
X-RAY DIFFRACTIONr_scangle_other14.4743.9531447
X-RAY DIFFRACTIONr_long_range_B_refined14.62223.642349
X-RAY DIFFRACTIONr_long_range_B_other14.75121.812305
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 147 -
Rwork0.222 2712 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8496-0.4049-0.25040.80870.30350.8171-0.0528-0.0665-0.00610.05310.03970.03470.0342-0.06920.0130.01530.00560.00430.01870.00550.025923.94316.8248.06
20.44691.3881-0.78254.7915-1.94131.87960.1208-0.0537-0.04930.2155-0.2512-0.0755-0.35580.00940.13040.12460.0656-0.02370.15550.03950.182136.54429.419-6.922
313.4979-0.26210.3667.51691.61866.97570.02170.2307-0.8714-0.01240.06870.35870.4054-0.6206-0.09040.0736-0.0135-0.04880.0867-0.03370.145614.36113.1188.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2B1 - 9
2X-RAY DIFFRACTION3P241 - 249

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