EMDB-16876: Structure of the Tau-PAM4 Type 1 amyloid fibril

Basic information

Entry

Database: EMDB / ID: EMD-16876

• Title: Structure of the Tau-PAM4 Type 1 amyloid fibril
• Map data: Final postprocess, sharpened, helical symmetrised map of the acetyl-TauPAM4 2PF fibril form

Sample

• Complex: 2PF amyloid fibril assembly of Tau-PAM4 peptide
  • Protein or peptide: Microtubule-associated protein tauTau protein
• Ligand: water

• Keywords: amyloid / tau / helical / cross-beta / fibril / neurodegeneration / PROTEIN FIBRIL

Function / homology

Function:

plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / 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 / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / intracellular distribution of mitochondria / axonal transport of mitochondrion / 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 / negative regulation of mitochondrial membrane potential / apolipoprotein binding / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / stress granule assembly / regulation of cellular response to heat / axon cytoplasm / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / 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 / synapse organization / response to lead ion / microglial cell activation / regulation of synaptic plasticity / Hsp90 protein binding / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / 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: synthetic construct (others)
• Method: helical reconstruction / cryo EM / Resolution: 2.6 Å
• Authors: Wilkinson M / Louros N / Tsaka G / Ramakers M / Morelli C / Garcia T / Gallardo RU / D'Haeyer S / Goossens V / Audenaert D / Thal DR / Ranson NA / Radford SE / Rousseau F / Schymkowitz J

Funding support

Belgium, 1 items

Organization	Grant number	Country
Research Foundation - Flanders (FWO)		Belgium

• Citation: Journal: Nat Commun / Year: 2024; Title: Local structural preferences in shaping tau amyloid polymorphism.; Authors: Nikolaos Louros / Martin Wilkinson / Grigoria Tsaka / Meine Ramakers / Chiara Morelli / Teresa Garcia / Rodrigo Gallardo / Sam D'Haeyer / Vera Goossens / Dominique Audenaert / Dietmar Rudolf Thal / Ian R Mackenzie / Rosa Rademakers / Neil A Ranson / Sheena E Radford / Frederic Rousseau / Joost Schymkowitz / ; Abstract: Tauopathies encompass a group of neurodegenerative disorders characterised by diverse tau amyloid fibril structures. The persistence of polymorphism across tauopathies suggests that distinct pathological conditions dictate the adopted polymorph for each disease. However, the extent to which intrinsic structural tendencies of tau amyloid cores contribute to fibril polymorphism remains uncertain. Using a combination of experimental approaches, we here identify a new amyloidogenic motif, PAM4 (Polymorphic Amyloid Motif of Repeat 4), as a significant contributor to tau polymorphism. Calculation of per-residue contributions to the stability of the fibril cores of different pathologic tau structures suggests that PAM4 plays a central role in preserving structural integrity across amyloid polymorphs. Consistent with this, cryo-EM structural analysis of fibrils formed from a synthetic PAM4 peptide shows that the sequence adopts alternative structures that closely correspond to distinct disease-associated tau strains. Furthermore, in-cell experiments revealed that PAM4 deletion hampers the cellular seeding efficiency of tau aggregates extracted from Alzheimer's disease, corticobasal degeneration, and progressive supranuclear palsy patients, underscoring PAM4's pivotal role in these tauopathies. Together, our results highlight the importance of the intrinsic structural propensity of amyloid core segments to determine the structure of tau in cells, and in propagating amyloid structures in disease.

History

Deposition	Mar 20, 2023	-
Header (metadata) release	Feb 21, 2024	-
Map release	Feb 21, 2024	-
Update	Feb 21, 2024	-
Current status	Feb 21, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_16876.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Final postprocess, sharpened, helical symmetrised map of the acetyl-TauPAM4 2PF fibril form
• Voxel size: X=Y=Z: 0.95 Å

Density

Contour Level	By AUTHOR: 0.014
Minimum - Maximum	-0.029934278 - 0.07028708
Average (Standard dev.)	0.0003623755 (±0.0035781835)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 300 300 300 Spacing 300 300 300
Cell	A=B=C: 285.0 Å α=β=γ: 90.0 °

Supplemental data

Half map: halfmap1

• File: emd_16876_half_map_1.map
• Annotation: halfmap1

Half map: halfmap2

• File: emd_16876_half_map_2.map
• Annotation: halfmap2

Sample components

Entire : 2PF amyloid fibril assembly of Tau-PAM4 peptide

• Entire: Name: 2PF amyloid fibril assembly of Tau-PAM4 peptide

Components

• Complex: 2PF amyloid fibril assembly of Tau-PAM4 peptide
  • Protein or peptide: Microtubule-associated protein tauTau protein
• Ligand: water

Supramolecule #1: 2PF amyloid fibril assembly of Tau-PAM4 peptide

• Supramolecule: Name: 2PF amyloid fibril assembly of Tau-PAM4 peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Synthesised peptide assembled into amyloid fibril
• Source (natural): Organism: synthetic construct (others)

Macromolecule #1: Microtubule-associated protein tau

• Macromolecule: Name: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 ; Details: 13-residue peptide of the PAM4 motif of Tau, corresponding to residues 350-362 of the Tau repeat domain. The peptide is N-terminally acetylated and C-terminally amidated; Number of copies: 36 / Enantiomer: LEVO
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 1.437622 KDa

Sequence

String:

(ACE)VQSKIGSLD NITH(NH2)

UniProtKB: Microtubule-associated protein tau

Macromolecule #2: water

• Macromolecule: Name: water / type: ligand / ID: 2 / Number of copies: 30 / Formula: HOH
• Molecular weight: Theoretical: 18.015 Da

Chemical component information

ChemComp-HOH:
WATER / Water

Experimental details

Structure determination

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

Sample preparation

• Concentration: 2.5 mg/mL
• Buffer: pH: 7 ; Details: Peptide resuspended in MilliQ water for aggregation reaction
• Grid: Model: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 130000
• Specialist optics: Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1512 / Average exposure time: 5.0 sec. / Average electron dose: 39.0 e/Ų; Details: Movies were collected as 1539 EER frames compressed and re-grouped into 36 TIF fractions
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: INSILICO MODEL; In silico model: Initial model generated from a single 2D class average from within the data
• Final angle assignment: Type: NOT APPLICABLE / Software - Name: RELION (ver. 4.0)
• Final reconstruction: Applied symmetry - Helical parameters - Δz: 4.86 Å; Applied symmetry - Helical parameters - Δ&Phi: -0.68 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 17820

Atomic model buiding 1

• Details: Initial model built manually in coot, no starting template
• Refinement: Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 54 / Target criteria: Cross-correlation coefficient

Output model

PDB-8oh2:
Structure of the Tau-PAM4 Type 1 amyloid fibril