EMDB-45008: Paired Helical Filaments purified from Down Syndrome individual b...

Basic information

Entry

Database: EMDB / ID: EMD-45008

• Title: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids

Sample

• Tissue: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids
  • Protein or peptide: Microtubule-associated protein tau

• Keywords: Amyloid / filament / neurodegeneration / Down syndrome / PROTEIN FIBRIL

Function / homology

Function:

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 / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / 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 / main axon / apolipoprotein binding / protein polymerization / axolemma / glial cell projection / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / neurofibrillary tangle assembly / positive regulation of axon extension / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / somatodendritic compartment / axon cytoplasm / positive regulation of microtubule polymerization / astrocyte activation / phosphatidylinositol binding / stress granule assembly / nuclear periphery / regulation of microtubule cytoskeleton organization / protein phosphatase 2A binding / cellular response to reactive oxygen species / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / synapse organization / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / response to lead ion / SH3 domain binding / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / microtubule cytoskeleton / growth cone / actin binding / cell body / double-stranded DNA binding / protein-macromolecule adaptor activity / microtubule binding / sequence-specific DNA binding / dendritic spine / amyloid fibril formation / microtubule / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / 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

Domain/homology:

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. / :

Component:

Microtubule-associated protein tau

• Biological species: Homo sapiens (human)
• Method: helical reconstruction / cryo EM / Resolution: 3.1 Å
• Authors: Tse E / Ghosh U / Condello C / Southworth D

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	RF1NS133651	United States

• Citation: Journal: Acta Neuropathol Commun / Year: 2024; Title: Cryo-EM structures reveal tau filaments from Down syndrome adopt Alzheimer's disease fold.; Authors: Ujjayini Ghosh / Eric Tse / Hyunjun Yang / Marie Shi / Christoffer D Caro / Feng Wang / Gregory E Merz / Stanley B Prusiner / Daniel R Southworth / Carlo Condello / ; Abstract: Down syndrome (DS) is a common genetic condition caused by trisomy of chromosome 21. Among their complex clinical features, including musculoskeletal, neurological, and cardiovascular disabilities, individuals with DS have an increased risk of developing progressive dementia and early-onset Alzheimer's disease (AD). This dementia is attributed to the increased gene dosage of the amyloid-β (Aβ) precursor protein gene, the formation of self-propagating Aβ and tau prion conformers, and the deposition of neurotoxic Aβ plaques and tau neurofibrillary tangles. Tau amyloid fibrils have previously been established to adopt many distinct conformations across different neurodegenerative conditions. Here, we report the characterization of brain samples from four DS cases spanning 36-63 years of age by spectral confocal imaging with conformation-specific dyes and cryo-electron microscopy (cryo-EM) to determine structures of isolated tau fibrils. High-resolution structures revealed paired helical filament (PHF) and straight filament (SF) conformations of tau that were identical to those determined from AD cases. The PHFs and SFs are made of two C-shaped protofilaments, each containing a cross-β/β-helix motif. Similar to filaments from AD cases, most filaments from the DS cases adopted the PHF form, while a minority (approximately 20%) formed SFs. Samples from the youngest individual with no documented dementia had sparse tau deposits. To isolate tau for cryo-EM from this challenging sample we used a novel affinity-grid method involving a graphene oxide surface derivatized with anti-tau antibodies. This method improved isolation and revealed that primarily tau PHFs and a minor population of chronic traumatic encephalopathy type II-like filaments were present in this youngest case. These findings expand the similarities between AD and DS to the molecular level, providing insight into their related pathologies and the potential for targeting common tau filament folds by small-molecule therapeutics and diagnostics.

History

Deposition	May 22, 2024	-
Header (metadata) release	Aug 14, 2024	-
Map release	Aug 14, 2024	-
Update	Aug 14, 2024	-
Current status	Aug 14, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_45008.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.834 Å

Density

Contour Level	By AUTHOR: 0.00793
Minimum - Maximum	-0.037579823 - 0.07215839
Average (Standard dev.)	0.0001070525 (±0.0020664856)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 280 280 280 Spacing 280 280 280
Cell	A=B=C: 233.52 Å α=β=γ: 90.0 °

Supplemental data

Half map: #2

• File: emd_45008_half_map_1.map

Half map: #1

• File: emd_45008_half_map_2.map

Sample components

Entire : Paired Helical Filaments purified from Down Syndrome individual b...

• Entire: Name: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids

Components

• Tissue: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids
  • Protein or peptide: Microtubule-associated protein tau

Supramolecule #1: Paired Helical Filaments purified from Down Syndrome individual b...

• Supramolecule: Name: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids; type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: Microtubule-associated protein tau

• Macromolecule: Name: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 8.370578 KDa

Sequence

String:

GSVQIVYKPV DLSKVTSKCG SLGNIHHKPG GGQVEVKSEK LDFKDRVQSK IGSLDNITHV PGGGNKKIET HKLTFRE

UniProtKB: Microtubule-associated protein tau

Experimental details

Structure determination

• Method: cryo EM
• Processing: helical reconstruction
• Aggregation state: filament

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE
• Details: Sarkosyl extraction of insoluble tau from fresh-frozen frontal cortex samples from Down Syndrome individuals

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Applied symmetry - Helical parameters - Δz: 2.37 Å; Applied symmetry - Helical parameters - Δ&Phi: 179.5 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79599
• Startup model: Type of model: INSILICO MODEL / In silico model: relion_helix_inimodel2d; Details: selected class averages with similar views along filament length
• Final angle assignment: Type: NOT APPLICABLE