PDB-9bxq: Paired Helical Filaments purified from Down Syndrome individual b...

Basic information

• Entry: Database: PDB / ID: 9bxq
• Title: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids
• Components: Microtubule-associated protein tau
• Keywords: PROTEIN FIBRIL / Amyloid / filament / neurodegeneration / Down syndrome

Function / homology

Function:

plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / generation of neurons / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of chromosome organization / regulation of mitochondrial fission / axonal transport of mitochondrion / intracellular distribution of mitochondria / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / glial cell projection / apolipoprotein binding / negative regulation of mitochondrial membrane potential / protein polymerization / axolemma / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of cellular response to heat / stress granule assembly / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / microtubule cytoskeleton organization / SH3 domain binding / cellular response to reactive oxygen species / cytoplasmic ribonucleoprotein granule / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding

Domain/homology:

: / 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.

Component:

Microtubule-associated protein tau

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

Funding support

United States, 1items

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	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release

Assembly

Deposited unit

C: Microtubule-associated protein tau

D: Microtubule-associated protein tau

E: Microtubule-associated protein tau

F: Microtubule-associated protein tau

G: Microtubule-associated protein tau

H: Microtubule-associated protein tau

Summary:

• 50.2 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,223	6
Polymers	50,223	6
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author
• Evidence: electron microscopy, not applicable

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555		1

Components

#1: Protein

C D E F G H
Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau

Details:

Mass: 8370.578 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10636

Experimental details

Experiment

• Experiment: Method: ELECTRON MICROSCOPY
• EM experiment: Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

Sample preparation

• Component: Name: Paired Helical Filaments purified from Down Syndrome individual brain tissue applied to graphene oxide antibody affinity grids; Type: TISSUE / Entity ID: all / Source: NATURAL
• Source (natural): Organism: Homo sapiens (human)
• Buffer solution: pH: 7.4
• Specimen: Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES; Details: Sarkosyl extraction of insoluble tau from fresh-frozen frontal cortex samples from Down Syndrome individuals
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Microscopy: Model: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
• Electron lens: Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 70 µm
• Image recording: Electron dose: 56 e/Ų / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
• EM imaging optics: Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

Processing

• EM software: Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement
• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Helical symmerty: Angular rotation/subunit: 179.5 ° / Axial rise/subunit: 2.37 Å / Axial symmetry: C1
• 3D reconstruction: Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79599 / Symmetry type: HELICAL

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
ELECTRON MICROSCOPY	f_bond_d	0.003	3576
ELECTRON MICROSCOPY	f_angle_d	0.683	4782
ELECTRON MICROSCOPY	f_dihedral_angle_d	5.33	474
ELECTRON MICROSCOPY	f_chiral_restr	0.05	534
ELECTRON MICROSCOPY	f_plane_restr	0.002	612