EMDB-42886: Cryo-EM structure of tau filaments made from jR2R3-P301L peptides...

Basic information

Entry

Database: EMDB / ID: EMD-42886

• Title: Cryo-EM structure of tau filaments made from jR2R3-P301L peptides induced with heparin

Sample

• Cell: Filament of tau jR2R3-P301L peptide indued with heparin
  • Protein or peptide: Microtubule-associated protein tau

• Keywords: tau / amyloid / filament / P301L / PROTEIN FIBRIL

Function / homology

Function:

plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / main axon / axonal transport / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of long-term synaptic depression / central nervous system neuron development / intracellular distribution of mitochondria / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / apolipoprotein binding / axolemma / protein polymerization / glial cell projection / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / neurofibrillary tangle assembly / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / supramolecular fiber organization / synapse assembly / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / regulation of calcium-mediated signaling / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / axon cytoplasm / stress granule assembly / phosphatidylinositol binding / regulation of microtubule cytoskeleton organization / nuclear periphery / protein phosphatase 2A binding / positive regulation of superoxide anion generation / cellular response to reactive oxygen species / astrocyte activation / Hsp90 protein binding / microglial cell activation / response to lead ion / cellular response to nerve growth factor stimulus / synapse organization / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / actin binding / cellular response to heat / microtubule cytoskeleton / cell body / growth cone / double-stranded DNA binding / protein-macromolecule adaptor activity / microtubule binding / dendritic spine / sequence-specific DNA binding / amyloid fibril formation / microtubule / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / 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: 3.0 Å
• Authors: Vigers M / Han S

Funding support

United States, 2 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM136411	United States
National Institutes of Health/Office of the Director	U24GM129547	United States

• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2025; Title: Water-directed pinning is key to tau prion formation.; Authors: Michael P Vigers / Samuel Lobo / Saeed Najafi / Austin Dubose / Karen Tsay / Pritam Ganguly / Andrew P Longhini / Yingying Jin / Steven K Buratto / Kenneth S Kosik / M Scott Shell / Joan-Emma Shea / Songi Han / ; Abstract: Tau forms fibrillar aggregates that are pathological hallmarks of a family of neurodegenerative diseases known as tauopathies. The synthetic replication of disease-specific fibril structures is a critical gap for developing diagnostic and therapeutic tools. This study debuts a strategy of identifying a critical and minimal folding motif in fibrils characteristic of tauopathies and generating seeding-competent fibrils from the isolated tau peptides. The 19-residue jR2R3 peptide (295 to 313) which spans the R2/R3 splice junction of tau, and includes the P301L mutation, is one such peptide that forms prion-competent fibrils. This tau fragment contains the hydrophobic VQIVYK hexapeptide that is part of the core of all known pathological tau fibril structures and an intramolecular counterstrand that stabilizes the strand-loop-strand (SLS) motif observed in 4R tauopathy fibrils. This study shows that P301L exhibits a duality of effects: it lowers the barrier for the peptide to adopt aggregation-prone conformations and enhances the local structuring of water around the mutation site to facilitate site-directed pinning and dewetting around sites 300-301 to achieve in-register stacking of tau to cross β-sheets. We solved a 3 Å cryo-EM structure of jR2R3-P301L fibrils in which each protofilament layer contains two jR2R3-P301L copies, of which one adopts a SLS fold found in 4R tauopathies and the other wraps around the SLS fold to stabilize it, reminiscent of the three- and fourfold structures observed in 4R tauopathies. These jR2R3-P301L fibrils are competent to template full-length 4R tau in a prion-like manner.

History

Deposition	Nov 20, 2023	-
Header (metadata) release	Dec 11, 2024	-
Map release	Dec 11, 2024	-
Update	Jun 25, 2025	-
Current status	Jun 25, 2025	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_42886.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.064 Å

Density

Contour Level	By AUTHOR: 10.92
Minimum - Maximum	-18.490438000000001 - 36.634253999999999
Average (Standard dev.)	0.000000000000272 (±1.0)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 408.576 Å α=β=γ: 90.0 °

Supplemental data

Half map: #1

• File: emd_42886_half_map_1.map

Half map: #2

• File: emd_42886_half_map_2.map

Sample components

Entire : Filament of tau jR2R3-P301L peptide indued with heparin

• Entire: Name: Filament of tau jR2R3-P301L peptide indued with heparin

Components

• Cell: Filament of tau jR2R3-P301L peptide indued with heparin
  • Protein or peptide: Microtubule-associated protein tau

Supramolecule #1: Filament of tau jR2R3-P301L peptide indued with heparin

• Supramolecule: Name: Filament of tau jR2R3-P301L peptide indued with heparin; type: cell / 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: 12 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 2.026359 KDa

Sequence

String:

DNIKHVLGGG SVQIVYKPV

UniProtKB: Microtubule-associated protein tau

Experimental details

Structure determination

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

Sample preparation

Buffer

pH: 7.4
Component:

Concentration	Formula	Name
50.0 mM	NaCl	sodium chloride
20.0 mM	NH4COOH	ammonium acetate

Details: 20mM ammoniium acetate, 50mM NaCl

• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average exposure time: 3.129 sec. / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Applied symmetry - Helical parameters - Δz: 2.39 Å; Applied symmetry - Helical parameters - Δ&Phi: 179.43 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 85235
• CTF correction: Software - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: OTHER
• Final angle assignment: Type: NOT APPLICABLE