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- PDB-8kdx: Tau-S214 Phosphorylation Inhibits Fyn Kinase Interaction and Incr... -

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Basic information

Entry
Database: PDB / ID: 8kdx
TitleTau-S214 Phosphorylation Inhibits Fyn Kinase Interaction and Increases the Decay Time of NMDAR-mediated Current
Components
  • Microtubule-associated protein tau
  • Tyrosine-protein kinase Fyn
KeywordsPEPTIDE BINDING PROTEIN / Alzheimer's disease / Fyn Kinase / SH3 Domain / Tau Protein and PXXP motif.
Function / homology
Function and homology information


response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / G protein-coupled glutamate receptor signaling pathway / Platelet Adhesion to exposed collagen / CD28 co-stimulation / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / negative regulation of dendritic spine maintenance / feeding behavior / Nef and signal transduction / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / dendrite morphogenesis / DCC mediated attractive signaling / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / Ephrin signaling / plus-end-directed organelle transport along microtubule / dendritic spine maintenance / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / Regulation of KIT signaling / generation of neurons / regulation of chromosome organization / tau-protein kinase activity / positive regulation of protein localization / CTLA4 inhibitory signaling / rRNA metabolic process / internal protein amino acid acetylation / leukocyte migration / phospholipase activator activity / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / regulation of mitochondrial fission / intracellular distribution of mitochondria / cellular response to platelet-derived growth factor stimulus / axonal transport of mitochondrion / axon development / Dectin-2 family / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / dynactin binding / CD28 dependent PI3K/Akt signaling / apolipoprotein binding / phospholipase binding / response to amyloid-beta / glial cell projection / negative regulation of mitochondrial membrane potential / Sema3A PAK dependent Axon repulsion / cellular response to glycine / FCGR activation / protein polymerization / alpha-tubulin binding / negative regulation of mitochondrial fission / EPH-ephrin mediated repulsion of cells / axolemma / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of axon extension / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / supramolecular fiber organization / regulation of cellular response to heat / stress granule assembly
Similarity search - Function
: / Fyn/Yrk, SH3 domain / : / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / SH3 domain / SH2 domain ...: / Fyn/Yrk, SH3 domain / : / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn / Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsPadavattan, S. / Jos, S.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Tau-S214 Phosphorylation Inhibits Fyn Kinase Interaction and Increases the Decay Time of NMDAR-mediated Current.
Authors: Jos, S. / Poulose, R. / Kambaru, A. / Gogoi, H. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B. / Mehta, B. / Padavattan, S.
History
DepositionAug 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn
B: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)8,4972
Polymers8,4972
Non-polymers00
Water2,396133
1
A: Tyrosine-protein kinase Fyn

B: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)8,4972
Polymers8,4972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area4600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.152, 35.558, 73.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 6884.386 Da / Num. of mol.: 1 / Fragment: FynSH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1612.810 Da / Num. of mol.: 1 / Fragment: Tau Peptide 207-221 / Source method: obtained synthetically / Details: GSRSR density not observed. / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.5 % / Description: orthorhombic space group P212121
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M Sodium citrate tribasic dehydrated, 0.1 M Tris buffer pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.01→32.002 Å / Num. obs: 43333 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.99 / Net I/σ(I): 32.1
Reflection shellResolution: 1.01→1.03 Å / Num. unique obs: 2839 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→32.002 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.178 / SU B: 0.698 / SU ML: 0.017 / Average fsc free: 0.9742 / Average fsc work: 0.9777 / Cross valid method: FREE R-VALUE / ESU R: 0.024 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1854 2142 4.951 %
Rwork0.1728 41123 -
all0.173 --
obs-43265 99.556 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.752 Å2-0 Å20 Å2
2---0.205 Å20 Å2
3----0.547 Å2
Refinement stepCycle: LAST / Resolution: 1.01→32.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms555 0 0 133 688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.012616
X-RAY DIFFRACTIONr_bond_other_d0.0010.016533
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.69854
X-RAY DIFFRACTIONr_angle_other_deg0.8071.5811245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.576580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.67253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8751090
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6271031
X-RAY DIFFRACTIONr_chiral_restr0.1130.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02144
X-RAY DIFFRACTIONr_nbd_refined0.2970.292
X-RAY DIFFRACTIONr_symmetry_nbd_other0.240.2512
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2288
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.260.295
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4660.216
X-RAY DIFFRACTIONr_nbd_other0.3060.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3780.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_mcbond_it1.5750.916290
X-RAY DIFFRACTIONr_mcbond_other1.5730.915290
X-RAY DIFFRACTIONr_mcangle_it2.2771.64362
X-RAY DIFFRACTIONr_mcangle_other2.2811.641363
X-RAY DIFFRACTIONr_scbond_it2.2821.095326
X-RAY DIFFRACTIONr_scbond_other2.2791.093327
X-RAY DIFFRACTIONr_scangle_it3.2761.923486
X-RAY DIFFRACTIONr_scangle_other3.2731.92487
X-RAY DIFFRACTIONr_lrange_it7.14817.862752
X-RAY DIFFRACTIONr_lrange_other6.93614.243700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.0360.3041480.2792839X-RAY DIFFRACTION94.946
1.036-1.0650.2241640.2182905X-RAY DIFFRACTION99.4169
1.065-1.0950.1971480.1922848X-RAY DIFFRACTION99.9666
1.095-1.1290.181550.1722760X-RAY DIFFRACTION99.9314
1.129-1.1660.1671220.1562706X-RAY DIFFRACTION100
1.166-1.2070.1691460.1562609X-RAY DIFFRACTION100
1.207-1.2520.1821190.1582529X-RAY DIFFRACTION100
1.252-1.3030.1661350.1572437X-RAY DIFFRACTION100
1.303-1.3610.1871020.1572346X-RAY DIFFRACTION100
1.361-1.4280.128992261X-RAY DIFFRACTION99.9576
1.428-1.5050.1741080.1542118X-RAY DIFFRACTION100
1.505-1.5960.1781120.1542019X-RAY DIFFRACTION100
1.596-1.7060.169980.1581904X-RAY DIFFRACTION100
1.706-1.8420.185970.1651780X-RAY DIFFRACTION100
1.842-2.0170.159881631X-RAY DIFFRACTION99.9419
2.017-2.2540.161740.1561519X-RAY DIFFRACTION99.8746
2.254-2.60.189710.1761335X-RAY DIFFRACTION100
2.6-3.180.212680.1931134X-RAY DIFFRACTION100
3.18-4.4750.174550.158902X-RAY DIFFRACTION99.7915
4.475-50.251330.246541X-RAY DIFFRACTION98.9655
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)
10.2786-0.22260.05531.0637-0.2132.22890.0389-0.0008-0.01670.0013-0.0329-0.0534-0.05090.1226-0.0060.0575-0.00640.00350.00920.00010.00850.3858.3-12.684
23.905-1.21052.60075.15090.57792.18130.0299-0.2461-0.1984-0.21360.1687-0.04720.0485-0.1115-0.19860.16870.0095-0.02810.1046-0.00230.06335.2296.3681.221
Refinement TLS groupSelection: ALL

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