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- PDB-9gg7: Crystal structure of 14-3-3 sigma dC - C38N in complex with Tau p... -

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Basic information

Entry
Database: PDB / ID: 9gg7
TitleCrystal structure of 14-3-3 sigma dC - C38N in complex with Tau pS324 peptide and covalent stabilizer 187
Components
  • 14-3-3 protein sigma
  • Isoform Tau-G of 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
Chem-TW8 / Microtubule-associated protein tau / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
Authorsvan den Oetelaar, M.C.M. / van de Wijngaart, T.R. / 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
B: 14-3-3 protein sigma
C: Isoform Tau-G of Microtubule-associated protein tau
P: Isoform Tau-G of Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8426
Polymers56,2374
Non-polymers6052
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-27 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.240, 62.472, 69.291
Angle α, β, γ (deg.)90.00, 107.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26553.875 Da / Num. of mol.: 2
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 Isoform Tau-G of Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1564.702 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Chemical ChemComp-TW8 / 4-(3,4-dihydro-2~{H}-quinoxalin-1-ylsulfonyl)benzaldehyde


Mass: 302.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Cocrystalization of 12 mg/ml protein, 2eq peptide and 1.8mM compound in 20 mM Sodium HEPES pH 7.5, 2 mM MgCl2, and 1.5 mM TCEP. Crystallization buffer: 0.19 M Calcium chloride dihydrate, 0. ...Details: Cocrystalization of 12 mg/ml protein, 2eq peptide and 1.8mM compound in 20 mM Sodium HEPES pH 7.5, 2 mM MgCl2, and 1.5 mM TCEP. Crystallization buffer: 0.19 M Calcium chloride dihydrate, 0.095 M Sodium HEPES pH 7.1, 5% glycerol, and28% PEG 400, mixed 1:1 with cocrystal mix

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.24→65.97 Å / Num. obs: 344584 / % possible obs: 97.5 % / Redundancy: 4.4 % / CC1/2: 0.981 / Net I/σ(I): 7.7
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 15878 / CC1/2: 0.414

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Processing

Software
NameVersionClassification
DIALS3.18.0data collection
Aimlessdata scaling
PHASERphasing
REFMAC5.7.0009refinement
Cootmodel building
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→45.38 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 7060 4.97 %RANDOM
Rwork0.2198 ---
obs0.2209 141935 89.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 0 398 4249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133927
X-RAY DIFFRACTIONf_angle_d1.7515285
X-RAY DIFFRACTIONf_dihedral_angle_d13.3561491
X-RAY DIFFRACTIONf_chiral_restr0.096576
X-RAY DIFFRACTIONf_plane_restr0.02686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.250.35942230.33054264X-RAY DIFFRACTION86
1.25-1.270.39712340.35214621X-RAY DIFFRACTION92
1.27-1.280.30642370.31884572X-RAY DIFFRACTION91
1.28-1.30.32272370.31154487X-RAY DIFFRACTION90
1.3-1.320.33972190.34607X-RAY DIFFRACTION92
1.32-1.340.28762490.27884640X-RAY DIFFRACTION92
1.34-1.350.28332140.28464623X-RAY DIFFRACTION92
1.35-1.370.30022550.30014570X-RAY DIFFRACTION91
1.37-1.40.24372510.27134589X-RAY DIFFRACTION92
1.4-1.420.2652730.25524610X-RAY DIFFRACTION92
1.42-1.440.282610.24754644X-RAY DIFFRACTION92
1.44-1.470.24762380.24094636X-RAY DIFFRACTION92
1.47-1.50.24032350.23624539X-RAY DIFFRACTION91
1.5-1.530.27332240.23754625X-RAY DIFFRACTION91
1.53-1.560.27942110.21654551X-RAY DIFFRACTION90
1.56-1.60.2232640.20444543X-RAY DIFFRACTION91
1.6-1.640.22542350.19934613X-RAY DIFFRACTION92
1.64-1.680.21072190.19214581X-RAY DIFFRACTION91
1.68-1.730.26592190.20354594X-RAY DIFFRACTION90
1.73-1.790.25282790.2024478X-RAY DIFFRACTION91
1.79-1.850.24582790.20944473X-RAY DIFFRACTION90
1.85-1.930.25562050.23284546X-RAY DIFFRACTION89
1.93-2.010.22972090.21734517X-RAY DIFFRACTION89
2.01-2.120.26412220.21124428X-RAY DIFFRACTION87
2.12-2.250.22092180.19284411X-RAY DIFFRACTION87
2.25-2.430.19982270.19914375X-RAY DIFFRACTION86
2.43-2.670.22432340.20314284X-RAY DIFFRACTION85
2.67-3.060.24552320.2264231X-RAY DIFFRACTION84
3.06-3.850.23912380.21344157X-RAY DIFFRACTION81
3.85-45.380.20862190.19654066X-RAY DIFFRACTION79

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