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- EMDB-7771: Cryo-EM reconstruction of microtubule-bound synthetic (R2x4) tau -

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Entry
Database: EMDB / ID: 7771
TitleCryo-EM reconstruction of microtubule-bound synthetic (R2x4) tau
Map dataCryo-EM reconstruction of microtubule-bound synthetic tau (R2x4)
SampleTernary complex of alpha-beta tubulin with synthetic (R2x4) tau
  • (Tubulin beta ...) x 2
  • (Tubulin alpha-1B ...) x 2
  • (Microtubule-associated protein ...) x 2
  • (ligand) x 3
Function / homologyTubulin/FtsZ, 2-layer sandwich domain / Beta tubulin, autoregulation binding site / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Resolution of Sister Chromatid Cohesion / Tubulin/FtsZ, C-terminal domain superfamily / Separation of Sister Chromatids / Tubulin, conserved site / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane ...Tubulin/FtsZ, 2-layer sandwich domain / Beta tubulin, autoregulation binding site / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Resolution of Sister Chromatid Cohesion / Tubulin/FtsZ, C-terminal domain superfamily / Separation of Sister Chromatids / Tubulin, conserved site / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Activation of AMPK downstream of NMDARs / Recruitment of mitotic centrosome proteins and complexes / Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP proteins tubulin-binding repeat signature. / Microtubule-associated protein Tau / Tubulin-beta mRNA autoregulation signal. / Tubulin subunits alpha, beta, and gamma signature. / Tubulin C-terminal domain / Tubulin/FtsZ, C-terminal / Tau and MAP protein, tubulin-binding repeat / Tubulin/FtsZ, GTPase domain superfamily / Tubulin / Tubulin/FtsZ family, GTPase domain / Loss of proteins required for interphase microtubule organization from the centrosome / Kinesins / Tubulin, C-terminal / Carboxyterminal post-translational modifications of tubulin / Beta tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Alpha tubulin / COPI-mediated anterograde transport / RHO GTPases Activate Formins / RHO GTPases activate IQGAPs / Intraflagellar transport / Anchoring of the basal body to the plasma membrane / Cilium Assembly / Hedgehog 'off' state / Recycling pathway of L1 / Recruitment of NuMA to mitotic centrosomes / Microtubule associated protein, tubulin-binding repeat / Tubulin/FtsZ, GTPase domain / plus-end-directed organelle transport along microtubule / positive regulation of diacylglycerol kinase activity / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / regulation of chromosome organization / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / rRNA metabolic process / tubulin complex / microtubule lateral binding / generation of neurons / negative regulation of mitochondrial fission / regulation of long-term synaptic depression / negative regulation of mitochondrial membrane potential / microtubule polymerization / lipoprotein particle binding / axonal transport of mitochondrion / intracellular distribution of mitochondria / axon development / positive regulation of cellular protein localization / negative regulation of tubulin deacetylation / AT DNA binding / regulation of mitochondrial fission / glial cell projection / central nervous system neuron development / regulation of calcium-mediated signaling / negative regulation of kinase activity / somatodendritic compartment / internal protein amino acid acetylation / regulation of microtubule polymerization / dynactin binding / stress granule assembly / receptor ligand activity / cellular response to brain-derived neurotrophic factor stimulus / axolemma / supramolecular fiber organization / cytoplasmic microtubule organization / main axon / regulation of microtubule polymerization or depolymerization / regulation of response to DNA damage stimulus / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / apolipoprotein binding / positive regulation of microtubule polymerization / axon cytoplasm / synapse assembly / phosphatidylinositol binding / microtubule-based process / amyloid fibril formation / microglial cell activation / nuclear periphery
Function and homology information
SourceSus scrofa (pig) / Homo sapiens (human) / Pig (pig)
Methodhelical reconstruction / cryo EM / 3.9 Å resolution
AuthorsNogales E / Kellogg EH
CitationJournal: Science / Year: 2018
Title: Near-atomic model of microtubule-tau interactions.
Authors: Elizabeth H Kellogg / Nisreen M A Hejab / Simon Poepsel / Kenneth H Downing / Frank DiMaio / Eva Nogales
Abstract: Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into ...Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into fibrils implicated in Alzheimer's disease. It is unclear which tau residues are crucial for tau-MT interactions, where tau binds on MTs, and how it stabilizes them. We used cryo-electron microscopy to visualize different tau constructs on MTs and computational approaches to generate atomic models of tau-tubulin interactions. The conserved tubulin-binding repeats within tau adopt similar extended structures along the crest of the protofilament, stabilizing the interface between tubulin dimers. Our structures explain the effect of phosphorylation on MT affinity and lead to a model of tau repeats binding in tandem along protofilaments, tethering together tubulin dimers and stabilizing polymerization interfaces.
Validation ReportPDB-ID: 6cvn

SummaryFull reportAbout validation report
DateDeposition: Mar 28, 2018 / Header (metadata) release: Apr 25, 2018 / Map release: May 23, 2018 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cvn
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6cvn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7771.map.gz (map file in CCP4 format, 322487 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
432 pix
1.32 Å/pix.
= 570.24 Å
432 pix
1.32 Å/pix.
= 570.24 Å
432 pix
1.32 Å/pix.
= 570.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.019 (by author), 0.019 (movie #1):
Minimum - Maximum-0.07416456 - 0.12162634
Average (Standard dev.)-0.00030287818 (0.0067039486)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions432432432
Origin0.00.00.0
Limit431.0431.0431.0
Spacing432432432
CellA=B=C: 570.24005 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z570.240570.240570.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ242496
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0740.122-0.000

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Supplemental data

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Sample components

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Entire Ternary complex of alpha-beta tubulin with synthetic (R2x4) tau

EntireName: Ternary complex of alpha-beta tubulin with synthetic (R2x4) tau
Number of components: 10

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Component #1: protein, Ternary complex of alpha-beta tubulin with synthetic (R2...

ProteinName: Ternary complex of alpha-beta tubulin with synthetic (R2x4) tau
Recombinant expression: No

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Component #2: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #3: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #4: protein, Microtubule-associated protein tau

ProteinName: Microtubule-associated protein tauTau protein / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 49.90777 kDa
SourceSpecies: Pig (pig)

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Component #6: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.204445 kDa
SourceSpecies: Pig (pig)

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Component #7: protein, Microtubule-associated protein tau

ProteinName: Microtubule-associated protein tauTau protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.534906 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

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Component #9: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #10: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 8.7 Å / Delta phi: -25.75 deg.
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 6.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 310.15 K / Humidity: 100 %
Details: blot force 10 pN, 6 second blot time. used C-flat 1.2/1.3 holey grids. First 2 uL of microtubules were adhered to grid for 30 seconds, followed by 2 4 uL washes of tau with 30 second incubation for each wash..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37878.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 812

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: real space correlation / Refinement space: REAL / Overall bvalue: 12
Output model

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