EMDB-16883: Structure of the Fmoc-Tau-PAM4 Type 3 amyloid fibril

Basic information

Entry

Database: EMDB / ID: EMD-16883

• Title: Structure of the Fmoc-Tau-PAM4 Type 3 amyloid fibril
• Map data: Final postprocessed, sharpened, helical symmetrised map of the Fmoc-TauPAM4 fibril morphology IIa

Sample

• Complex: Amyloid fibril form 2a of Tau-PAM4 peptide adducted with the Fmoc protection group
  • Protein or peptide: Microtubule-associated protein tau

• Keywords: amyloid / tau / helical / cross-beta / fibril / neurodegeneration / Fmoc / 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 / axonal transport / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex / 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 / 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 / dynactin binding / negative regulation of mitochondrial membrane potential / apolipoprotein binding / glial cell projection / axolemma / protein polymerization / 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 / synapse assembly / regulation of cellular response to heat / supramolecular fiber organization / positive regulation of protein localization / regulation of calcium-mediated signaling / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / axon cytoplasm / positive regulation of microtubule polymerization / 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 / cellular response to nerve growth factor stimulus / response to lead ion / 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 / microtubule binding / protein-macromolecule adaptor activity / dendritic spine / sequence-specific DNA binding / microtubule / amyloid fibril formation / 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: 2.7 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 21, 2023	-
Header (metadata) release	Feb 21, 2024	-
Map release	Feb 21, 2024	-
Update	Nov 27, 2024	-
Current status	Nov 27, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_16883.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Final postprocessed, sharpened, helical symmetrised map of the Fmoc-TauPAM4 fibril morphology IIa
• Voxel size: X=Y=Z: 0.94 Å

Density

Contour Level	By AUTHOR: 0.013
Minimum - Maximum	-0.022152433 - 0.05096678
Average (Standard dev.)	0.00025926903 (±0.002446436)

• 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: 282.0 Å α=β=γ: 90.0 °

Supplemental data

Half map: halfmap2

• File: emd_16883_half_map_1.map
• Annotation: halfmap2

Half map: halfmap1

• File: emd_16883_half_map_2.map
• Annotation: halfmap1

Sample components

Entire : Amyloid fibril form 2a of Tau-PAM4 peptide adducted with the Fmoc...

• Entire: Name: Amyloid fibril form 2a of Tau-PAM4 peptide adducted with the Fmoc protection group

Components

• Complex: Amyloid fibril form 2a of Tau-PAM4 peptide adducted with the Fmoc protection group
  • Protein or peptide: Microtubule-associated protein tau

Supramolecule #1: Amyloid fibril form 2a of Tau-PAM4 peptide adducted with the Fmoc...

• Supramolecule: Name: Amyloid fibril form 2a of Tau-PAM4 peptide adducted with the Fmoc protection group; type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Synthesised peptide assembled into amyloid fibril
• Source (natural): Organism: Homo sapiens (human)

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 C-terminally amidated and should have been N-terminally acetylated but 10% of the peptide (by mass spec) was still adducted to the Fmoc protection group from peptide synthesis. This contaminant species dominated fibril assembly; Number of copies: 24 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 1.652269 KDa

Sequence

String:

(VP1)VQSKIGSLD NITH(NH2)

UniProtKB: Microtubule-associated protein tau

Experimental details

Structure determination

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

Sample preparation

• Concentration: 0.6 mg/mL
• Buffer: pH: 7 ; Details: Peptide resuspended in MilliQ water for aggregation reaction
• Grid: Model: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / 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
• Specialist optics: Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
• 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: 1957 / Average exposure time: 5.0 sec. / Average electron dose: 32.0 e/Ų; Details: Movies were collected as 1204 EER frames compressed and re-grouped into 35 TIF fractions
• 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 FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Applied symmetry - Helical parameters - Δz: 4.8 Å; Applied symmetry - Helical parameters - Δ&Phi: -1.05 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 11319
• Segment selection: Number selected: 520390 / Software - Name: crYOLO (ver. 1.8)
• 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)

Atomic model buiding 1

• Details: Initial model built manually in coot, no starting template
• Refinement: Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 48 / Target criteria: Cross-correlation coefficient

Output model

PDB-8ohp:
Structure of the Fmoc-Tau-PAM4 Type 3 amyloid fibril