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- EMDB-21207: Paired Helical Filament from Alzheimer's Disease Human Brain Tissue -

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Basic information

Entry
Database: EMDB / ID: EMD-21207
TitlePaired Helical Filament from Alzheimer's Disease Human Brain Tissue
Map dataPaired Helical Filament from Alzheimer's Disease Human Brain Tissue
Sample
  • Tissue: Paired Helical Filament from Alzheimer's Disease Human Brain Tissue
    • Protein or peptide: Microtubule-associated protein tau
  • Ligand: GLYCINE
KeywordsPathological amyloid fibril cross-beta fold parallel beta-sheets / PROTEIN FIBRIL
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of protein localization to mitochondrion / 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 / negative regulation of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of microtubule-based movement / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / 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 / apolipoprotein binding / main axon / protein polymerization / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / glial cell projection / neurofibrillary tangle assembly / positive regulation of axon extension / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / positive regulation of superoxide anion generation / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / regulation of long-term synaptic depression / positive regulation of microtubule polymerization / cytoplasmic microtubule organization / synapse assembly / regulation of calcium-mediated signaling / somatodendritic compartment / axon cytoplasm / astrocyte activation / phosphatidylinositol binding / nuclear periphery / enzyme inhibitor activity / stress granule assembly / protein phosphatase 2A binding / regulation of microtubule cytoskeleton organization / cellular response to reactive oxygen species / microglial cell activation / Hsp90 protein binding / cellular response to nerve growth factor stimulus / protein homooligomerization / synapse organization / PKR-mediated signaling / regulation of synaptic plasticity / regulation of autophagy / SH3 domain binding / response to lead ion / microtubule cytoskeleton organization / memory / neuron projection development / cytoplasmic ribonucleoprotein granule / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / microtubule cytoskeleton / actin binding / growth cone / cell body / double-stranded DNA binding / microtubule binding / protein-macromolecule adaptor activity / sequence-specific DNA binding / amyloid fibril formation / dendritic spine / microtubule / learning or memory / neuron projection / 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
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: 3.3 Å
AuthorsArakhamia T / Lee CE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: Cell / Year: 2020
Title: Posttranslational Modifications Mediate the Structural Diversity of Tauopathy Strains.
Authors: Tamta Arakhamia / Christina E Lee / Yari Carlomagno / Duc M Duong / Sean R Kundinger / Kevin Wang / Dewight Williams / Michael DeTure / Dennis W Dickson / Casey N Cook / Nicholas T Seyfried ...Authors: Tamta Arakhamia / Christina E Lee / Yari Carlomagno / Duc M Duong / Sean R Kundinger / Kevin Wang / Dewight Williams / Michael DeTure / Dennis W Dickson / Casey N Cook / Nicholas T Seyfried / Leonard Petrucelli / Anthony W P Fitzpatrick /
Abstract: Tau aggregation into insoluble filaments is the defining pathological hallmark of tauopathies. However, it is not known what controls the formation and templated seeding of strain-specific structures ...Tau aggregation into insoluble filaments is the defining pathological hallmark of tauopathies. However, it is not known what controls the formation and templated seeding of strain-specific structures associated with individual tauopathies. Here, we use cryo-electron microscopy (cryo-EM) to determine the structures of tau filaments from corticobasal degeneration (CBD) human brain tissue. Cryo-EM and mass spectrometry of tau filaments from CBD reveal that this conformer is heavily decorated with posttranslational modifications (PTMs), enabling us to map PTMs directly onto the structures. By comparing the structures and PTMs of tau filaments from CBD and Alzheimer's disease, it is found that ubiquitination of tau can mediate inter-protofilament interfaces. We propose a structure-based model in which cross-talk between PTMs influences tau filament structure, contributing to the structural diversity of tauopathy strains. Our approach establishes a framework for further elucidating the relationship between the structures of polymorphic fibrils, including their PTMs, and neurodegenerative disease.
History
DepositionJan 10, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseMar 4, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vhl
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21207.png

Downloads & links

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Map

FileDownload / File: emd_21207.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPaired Helical Filament from Alzheimer's Disease Human Brain Tissue
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 270 pix.
= 280.8 Å		1.04 Å/pix.
x 270 pix.
= 280.8 Å		1.04 Å/pix.
x 270 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.019938486 - 0.048748035
Average (Standard dev.)0.00007788765 (±0.0010540653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 280.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0200.0490.000

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Supplemental data

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Sample components

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Entire : Paired Helical Filament from Alzheimer's Disease Human Brain Tissue

EntireName: Paired Helical Filament from Alzheimer's Disease Human Brain Tissue
Components
  • Tissue: Paired Helical Filament from Alzheimer's Disease Human Brain Tissue
    • Protein or peptide: Microtubule-associated protein tau
  • Ligand: GLYCINE

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Supramolecule #1: Paired Helical Filament from Alzheimer's Disease Human Brain Tissue

SupramoleculeName: Paired Helical Filament from Alzheimer's Disease Human Brain Tissue
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.370578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GSVQIVYKPV DLSKVTSKCG SLGNIHHKPG GGQVEVKSEK LDFKDRVQSK IGSLDNITHV PGGGNKKIET HKLTFRE

UniProtKB: Microtubule-associated protein tau

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Macromolecule #2: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.353 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.417 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156840
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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