EMDB-28721: CryoEM structure of synthetic tau repeat R1R2 with two acetylated...

Basic information

Entry

Database: EMDB / ID: EMD-28721

• Title: CryoEM structure of synthetic tau repeat R1R2 with two acetylated lysines at positions 274 and 280

Sample

• Complex: Acetylated tau repeat 1 and 2 fragment (AcR1R2)
  • Protein or peptide: Acetylated tau repeat 1 and 2 fragment (AcR1R2)

• Keywords: Amyloid motif / acetylation / tau / repeat domain / post-translational modification / 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 / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex / positive regulation of protein localization to synapse / 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 / 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 / synapse assembly / 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 / 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 / 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 / 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: 3.88 Å
• Authors: Li L / Nguyen B / Mullapudi V / Saelices L / Joachimiak L

Funding support

United States, 3 items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	1U01CA242115	United States
Welch Foundation	I-1928-20200401	United States
Chan Zuckerberg Initiative	2018-191983	United States

• Citation: Journal: Structure / Year: 2023; Title: Disease-associated patterns of acetylation stabilize tau fibril formation.; Authors: Li Li / Binh A Nguyen / Vishruth Mullapudi / Yang Li / Lorena Saelices / Lukasz A Joachimiak / ; Abstract: Assembly of tau into beta-sheet-rich amyloids dictates the pathology of a diversity of diseases. Lysine acetylation has been proposed to drive tau amyloid assembly, but no direct mechanism has emerged. Using tau fragments, we identify patterns of acetylation that flank amyloidogenic motifs on the tau fragments that promote rapid fibril assembly. We determined a 3.9 Å cryo-EM amyloid fibril structure assembled from an acetylated tau fragment uncovering how lysine acetylation can mediate gain-of-function interactions. Comparison of the structure to an ex vivo tauopathy fibril reveals regions of structural similarity. Finally, we show that fibrils encoding disease-associated patterns of acetylation are active in cell-based tau aggregation assays. Our data uncover the dual role of lysine residues in limiting tau aggregation while their acetylation leads to stabilizing pro-aggregation interactions. Design of tau sequence with specific acetylation patterns may lead to controllable tau aggregation to direct folding of tau into distinct amyloid folds.

History

Deposition	Oct 29, 2022	-
Header (metadata) release	Mar 22, 2023	-
Map release	Mar 22, 2023	-
Update	Jan 17, 2024	-
Current status	Jan 17, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_28721.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.66 Å

Density

Contour Level	By AUTHOR: 0.043
Minimum - Maximum	-0.14425316 - 0.1799977
Average (Standard dev.)	0.0006178718 (±0.0059643527)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 180 180 180 Spacing 180 180 180
Cell	A=B=C: 298.8 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_28721_msk_1.map

Additional map: #1

• File: emd_28721_additional_1.map

Half map: #1

• File: emd_28721_half_map_1.map

Half map: #2

• File: emd_28721_half_map_2.map

Sample components

Entire : Acetylated tau repeat 1 and 2 fragment (AcR1R2)

• Entire: Name: Acetylated tau repeat 1 and 2 fragment (AcR1R2)

Components

• Complex: Acetylated tau repeat 1 and 2 fragment (AcR1R2)
  • Protein or peptide: Acetylated tau repeat 1 and 2 fragment (AcR1R2)

Supramolecule #1: Acetylated tau repeat 1 and 2 fragment (AcR1R2)

• Supramolecule: Name: Acetylated tau repeat 1 and 2 fragment (AcR1R2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all; Details: Synthetic tau repeat R1R2 with two acetylated lysines at position 274 and 280
• Source (natural): Organism: Homo sapiens (human) / Synthetically produced: Yes

Macromolecule #1: Acetylated tau repeat 1 and 2 fragment (AcR1R2)

• Macromolecule: Name: Acetylated tau repeat 1 and 2 fragment (AcR1R2) / type: protein_or_peptide / ID: 1 / Details: (ALY): Acetylated lysine / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)

Sequence

String:

TENLKHQPGG G(ALY)VQIIN(ALY)

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.4 / Details: PBS
• Grid: Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5901 / Average exposure time: 4.5 sec. / Average electron dose: 52.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: 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: 105000
• 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: 4.75 Å; Applied symmetry - Helical parameters - Δ&Phi: -1.00 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 45674
• Segment selection: Number selected: 1696844 / Software - Name: crYOLO (ver. 1.8) / Details: CrYOLO picked.
• Startup model: Type of model: OTHER / Details: Featureless cylinder
• Final angle assignment: Type: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)