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- EMDB-75271: VT Ia tau filament from VT Case 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-75271
TitleVT Ia tau filament from VT Case 1
Map data
Sample
  • Complex: tau filaments from VT
    • Protein or peptide: Microtubule-associated protein tau
KeywordsMicrotubule-associated protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / microtubule stabilizing activity / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / generation of neurons ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / microtubule stabilizing activity / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / generation of neurons / axonal transport of mitochondrion / axon development / rRNA metabolic process / central nervous system neuron development / regulation of microtubule-based movement / negative regulation of protein localization to mitochondrion / regulation of mitochondrial fission / regulation of chromosome organization / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / negative regulation of mitochondrial membrane potential / microtubule polymerization / regulation of microtubule polymerization / dynactin binding / apolipoprotein binding / regulation of calcium-mediated signaling / main axon / Caspase-mediated cleavage of cytoskeletal proteins / glial cell projection / regulation of microtubule polymerization or depolymerization / neurofibrillary tangle assembly / negative regulation of mitochondrial fission / protein polymerization / positive regulation of axon extension / axolemma / regulation of cellular response to heat / positive regulation of microtubule polymerization / positive regulation of superoxide anion generation / cytoplasmic microtubule organization / Activation of AMPK downstream of NMDARs / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / axon cytoplasm / positive regulation of protein localization / supramolecular fiber organization / synapse assembly / somatodendritic compartment / astrocyte activation / nuclear periphery / phosphatidylinositol binding / protein phosphatase 2A binding / stress granule assembly / enzyme inhibitor activity / SH3 domain binding / cellular response to reactive oxygen species / regulation of microtubule cytoskeleton organization / microtubule cytoskeleton organization / microglial cell activation / cellular response to nerve growth factor stimulus / memory / Hsp90 protein binding / regulation of autophagy / regulation of synaptic plasticity / protein homooligomerization / synapse organization / PKR-mediated signaling / response to lead ion / neuron projection development / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / cell-cell signaling / cellular response to heat / single-stranded DNA binding / actin binding / protein-folding chaperone binding / growth cone / double-stranded DNA binding / cell body / sequence-specific DNA binding / microtubule binding / amyloid fibril formation / dendritic spine / learning or memory / protein-macromolecule adaptor activity / membrane raft / negative regulation of gene expression / axon / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
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. / :
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsWatanabe R / Lee EB
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1 AG065341 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P30 AG072979 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142505 United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Repositioning of polyubiquitin alters the pathologic tau filament structure.
Authors: Ryohei Watanabe / Benjamin C Creekmore / Nabil F Darwich / Courtney L Smith / Hong Xu / Angelina Baltazar / Sacha Salphati / Lakshmi Changolkar / Kevt'her Hoxha / Bin Zhang / Caroline M ...Authors: Ryohei Watanabe / Benjamin C Creekmore / Nabil F Darwich / Courtney L Smith / Hong Xu / Angelina Baltazar / Sacha Salphati / Lakshmi Changolkar / Kevt'her Hoxha / Bin Zhang / Caroline M O'Rourke / George M Burslem / Virginia M-Y Lee / Yi-Wei Chang / Edward B Lee /
Abstract: Structurally diverse tau filaments form proteinaceous aggregates in a heterogeneous group of neurodegenerative diseases called tauopathies. The factors extrinsic to the highly ordered core structure ...Structurally diverse tau filaments form proteinaceous aggregates in a heterogeneous group of neurodegenerative diseases called tauopathies. The factors extrinsic to the highly ordered core structure that influence tau filament stability are not well understood. Here, we found that polyubiquitinated tau filaments from Alzheimer disease and vacuolar tauopathy human brain tissue exhibit distinct seeding patterns in mice, in association with differences in tau filament ultrastructure determined by cryo-electron microscopy. Chemical modulation of the polarity of polyubiquitin adjacent to the tau core with the small molecule ubistatin B resulted in the repositioning of poorly structured densities toward positively charged residues on the highly structured core filament, leading to shifting of the protofilament-protofilament interface of certain vacuolar tauopathy tau filaments. These results suggest that the structure of tau filaments that are associated with different seeding activities in vivo can be influenced by post-translational modifications.
History
DepositionJan 27, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75271.png

Downloads & links

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Map

FileDownload / File: emd_75271.map.gz / Format: CCP4 / Size: 28.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 50 pix.
= 54. Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0248
Minimum - Maximum-0.057839133 - 0.12736501
Average (Standard dev.)0.00047109206 (±0.004782795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions38438450
Spacing38438450
CellA: 414.72003 Å / B: 414.72003 Å / C: 54.000004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75271_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75271_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75271_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : tau filaments from VT

EntireName: tau filaments from VT
Components
  • Complex: tau filaments from VT
    • Protein or peptide: Microtubule-associated protein tau

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Supramolecule #1: tau filaments from VT

SupramoleculeName: tau filaments from VT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Microtubule-associated protein tau

MacromoleculeName: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.184412 KDa
SequenceString:
SVQIVYKPVD LSKVTSKCGS LGNIHHKPGG GQVEVKSEKL DFKDRVQSKI GSLDNITHVP GGGNKKIETH KLTFR

UniProtKB: Microtubule-associated protein tau

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.91 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailsSarkosyl-insoluble proteins were extracted from the frontal neocortex of the patient's brain.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 40.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.38 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 31989
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: A featureless cylinder was used as the initial reference map.
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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