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- PDB-8qdv: Structure of 14-3-3 zeta delta C with the bivalent tau-pS214-pS32... -

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Basic information

Entry
Database: PDB / ID: 8qdv
TitleStructure of 14-3-3 zeta delta C with the bivalent tau-pS214-pS324 peptide
Components
  • 14-3-3 protein zeta/delta
  • Microtubule-associated protein tau
KeywordsPROTEIN BINDING / 14-3-3 zeta / tau / protein-protein interaction
Function / homology
Function and homology information


synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / regulation of synapse maturation / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / plus-end-directed organelle transport along microtubule ...synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / regulation of synapse maturation / tube formation / Rap1 signalling / negative regulation of protein localization to nucleus / plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / GP1b-IX-V activation signalling / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / rRNA metabolic process / internal protein amino acid acetylation / regulation of chromosome organization / regulation of mitochondrial fission / axonal transport of mitochondrion / axon development / intracellular distribution of mitochondria / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / apolipoprotein binding / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / protein polymerization / axolemma / Activation of BAD and translocation to mitochondria / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / protein targeting / positive regulation of axon extension / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of microtubule cytoskeleton organization / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / regulation of cellular response to heat / cytoplasmic microtubule organization / stress granule assembly / supramolecular fiber organization / RHO GTPases activate PKNs / regulation of calcium-mediated signaling / axon cytoplasm / negative regulation of TORC1 signaling / somatodendritic compartment / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / phosphatidylinositol binding / regulation of ERK1 and ERK2 cascade / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / astrocyte activation / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / response to lead ion / Negative regulation of NOTCH4 signaling / lung development / microglial cell activation / synapse organization / Hsp90 protein binding / regulation of protein stability / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / memory / activation of cysteine-type endopeptidase activity involved in apoptotic process
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 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein ...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 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 zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: 14-3-3zeta binding increases cytosolic phospho-Tau solubility by decreasing its condensation, aggregation, and microtubule association
Authors: Hochmair, J. / van den Oetelaar, M.C.M. / Ravatt, R. / Lemmens, L.J.M. / Ponce, R. / Semenova, E. / Mohapatra, S. / Ottmann, C. / Diez, L. / Brunsveld, L. / Wegmann, S.
History
DepositionAug 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
C: Microtubule-associated protein tau
B: 14-3-3 protein zeta/delta
E: 14-3-3 protein zeta/delta
F: Microtubule-associated protein tau
G: 14-3-3 protein zeta/delta


Theoretical massNumber of molelcules
Total (without water)112,7776
Polymers112,7776
Non-polymers00
Water905
1
A: 14-3-3 protein zeta/delta
C: Microtubule-associated protein tau
B: 14-3-3 protein zeta/delta


Theoretical massNumber of molelcules
Total (without water)56,3883
Polymers56,3883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-23 kcal/mol
Surface area22530 Å2
MethodPISA
2
E: 14-3-3 protein zeta/delta
F: Microtubule-associated protein tau
G: 14-3-3 protein zeta/delta


Theoretical massNumber of molelcules
Total (without water)56,3883
Polymers56,3883
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-28 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.452, 59.898, 149.672
Angle α, β, γ (deg.)90.00, 113.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 3754.888 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium Fluoride, 0.1M bis-tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972425 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972425 Å / Relative weight: 1
ReflectionResolution: 2.5→137.59 Å / Num. obs: 43218 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 59.6 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4507 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→137.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.935 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26001 2185 5.1 %RANDOM
Rwork0.21615 ---
obs0.21831 41031 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.87 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å24.95 Å2
2---3.68 Å20 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.5→137.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7225 0 0 5 7230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127485
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166908
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.65310173
X-RAY DIFFRACTIONr_angle_other_deg0.4011.56515922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.529536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.273101236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1348.3433841
X-RAY DIFFRACTIONr_mcbond_other6.1338.3433841
X-RAY DIFFRACTIONr_mcangle_it8.86914.9674801
X-RAY DIFFRACTIONr_mcangle_other8.86814.9684802
X-RAY DIFFRACTIONr_scbond_it6.4488.6013644
X-RAY DIFFRACTIONr_scbond_other6.4478.6023645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.62915.6945349
X-RAY DIFFRACTIONr_long_range_B_refined11.56174.848416
X-RAY DIFFRACTIONr_long_range_B_other11.5674.858417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 158 -
Rwork0.329 3028 -
obs--99.78 %

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