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- EMDB-13223: Limbic-predominant neuronal inclusion body 4R tauopathy type 1a t... -

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Basic information

Entry
Database: EMDB / ID: EMD-13223
TitleLimbic-predominant neuronal inclusion body 4R tauopathy type 1a tau filament
Map data
Sample
  • Tissue: Sarkosyl-insoluble fraction from the temporal cortex of an individual with limbic-predominant neuronal inclusion body 4R tauopathy
    • Protein or peptide: Microtubule-associated protein tau
  • Ligand: water
KeywordsAmyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / : / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / positive regulation of protein localization to synapse / axonal transport / main axon ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / : / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / positive regulation of protein localization to synapse / axonal transport / main axon / phosphatidylinositol bisphosphate binding / tubulin complex / regulation of long-term synaptic depression / negative regulation of tubulin deacetylation / negative regulation of kinase activity / generation of neurons / internal protein amino acid acetylation / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / intracellular distribution of mitochondria / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / negative regulation of mitochondrial membrane potential / glial cell projection / apolipoprotein binding / protein polymerization / negative regulation of mitochondrial fission / axolemma / regulation of microtubule polymerization or depolymerization / Caspase-mediated cleavage of cytoskeletal proteins / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / synapse assembly / cytoplasmic microtubule organization / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / positive regulation of protein localization / supramolecular fiber organization / regulation of calcium-mediated signaling / axon cytoplasm / somatodendritic compartment / stress granule assembly / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of microtubule polymerization / phosphatidylinositol binding / nuclear periphery / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / cellular response to reactive oxygen species / response to lead ion / Hsp90 protein binding / microglial cell activation / synapse organization / cellular response to nerve growth factor stimulus / : / protein homooligomerization / regulation of synaptic plasticity / PKR-mediated signaling / memory / SH3 domain binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / microtubule cytoskeleton / cell-cell signaling / single-stranded DNA binding / actin binding / protein-folding chaperone binding / cellular response to heat / growth cone / protein-macromolecule adaptor activity / cell body / double-stranded DNA binding / microtubule binding / sequence-specific DNA binding / microtubule / amyloid fibril formation / 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
Similarity search - Function
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. / :
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsShi Y / Zhang W
Funding support United Kingdom, European Union, Japan, United States, 12 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184291 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1013 United Kingdom
Innovative Medicines Initiative116060European Union
Japan Science and TechnologyJPMJCR18H3 Japan
Japan Agency for Medical Research and Development (AMED)JP20dm0207072 Japan
Japan Agency for Medical Research and Development (AMED)JP21dk0207045 Japan
Japan Agency for Medical Research and Development (AMED)JP21ek0109545 Japan
Japan Agency for Medical Research and Development (AMED)JP20ek0109392 Japan
Japan Agency for Medical Research and Development (AMED)JP20ek0109391 Japan
National Institutes of Health/National Institute on Aging (NIH/NIA)P30-AG010133 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)UO1-NS110437 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1-AG071177 United States
CitationJournal: Nature / Year: 2021
Title: Structure-based classification of tauopathies.
Authors: Yang Shi / Wenjuan Zhang / Yang Yang / Alexey G Murzin / Benjamin Falcon / Abhay Kotecha / Mike van Beers / Airi Tarutani / Fuyuki Kametani / Holly J Garringer / Ruben Vidal / Grace I ...Authors: Yang Shi / Wenjuan Zhang / Yang Yang / Alexey G Murzin / Benjamin Falcon / Abhay Kotecha / Mike van Beers / Airi Tarutani / Fuyuki Kametani / Holly J Garringer / Ruben Vidal / Grace I Hallinan / Tammaryn Lashley / Yuko Saito / Shigeo Murayama / Mari Yoshida / Hidetomo Tanaka / Akiyoshi Kakita / Takeshi Ikeuchi / Andrew C Robinson / David M A Mann / Gabor G Kovacs / Tamas Revesz / Bernardino Ghetti / Masato Hasegawa / Michel Goedert / Sjors H W Scheres /
Abstract: The ordered assembly of tau protein into filaments characterizes several neurodegenerative diseases, which are called tauopathies. It was previously reported that, by cryo-electron microscopy, the ...The ordered assembly of tau protein into filaments characterizes several neurodegenerative diseases, which are called tauopathies. It was previously reported that, by cryo-electron microscopy, the structures of tau filaments from Alzheimer's disease, Pick's disease, chronic traumatic encephalopathy and corticobasal degeneration are distinct. Here we show that the structures of tau filaments from progressive supranuclear palsy (PSP) define a new three-layered fold. Moreover, the structures of tau filaments from globular glial tauopathy are similar to those from PSP. The tau filament fold of argyrophilic grain disease (AGD) differs, instead resembling the four-layered fold of corticobasal degeneration. The AGD fold is also observed in ageing-related tau astrogliopathy. Tau protofilament structures from inherited cases of mutations at positions +3 or +16 in intron 10 of MAPT (the microtubule-associated protein tau gene) are also identical to those from AGD, suggesting that relative overproduction of four-repeat tau can give rise to the AGD fold. Finally, the structures of tau filaments from cases of familial British dementia and familial Danish dementia are the same as those from cases of Alzheimer's disease and primary age-related tauopathy. These findings suggest a hierarchical classification of tauopathies on the basis of their filament folds, which complements clinical diagnosis and neuropathology and also allows the identification of new entities-as we show for a case diagnosed as PSP, but with filament structures that are intermediate between those of globular glial tauopathy and PSP.
History
DepositionJul 15, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p6a
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p6a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13223.png

Downloads & links

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Map

FileDownload / File: emd_13223.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 340 pix.
= 247.18 Å		0.73 Å/pix.
x 340 pix.
= 247.18 Å		0.73 Å/pix.
x 340 pix.
= 247.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.036840804 - 0.0925913
Average (Standard dev.)0.00027527643 (±0.0038160034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 247.18 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.7270.7270.727
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z247.180247.180247.180
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0370.0930.000

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Supplemental data

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Mask #1

Fileemd_13223_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13223_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13223_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sarkosyl-insoluble fraction from the temporal cortex of an indivi...

EntireName: Sarkosyl-insoluble fraction from the temporal cortex of an individual with limbic-predominant neuronal inclusion body 4R tauopathy
Components
  • Tissue: Sarkosyl-insoluble fraction from the temporal cortex of an individual with limbic-predominant neuronal inclusion body 4R tauopathy
    • Protein or peptide: Microtubule-associated protein tau
  • Ligand: water

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Supramolecule #1: Sarkosyl-insoluble fraction from the temporal cortex of an indivi...

SupramoleculeName: Sarkosyl-insoluble fraction from the temporal cortex of an individual with limbic-predominant neuronal inclusion body 4R tauopathy
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Microtubule-associated protein tau

MacromoleculeName: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.919871 KDa
SequenceString: MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKSTP TAEDVTAPLV DEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA GHVTQARMVS KSKDGTGSDD KKAKGADGKT KIATPRGAAP P GQKGQANA ...String:
MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKSTP TAEDVTAPLV DEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA GHVTQARMVS KSKDGTGSDD KKAKGADGKT KIATPRGAAP P GQKGQANA TRIPAKTPPA PKTPPSSGEP PKSGDRSGYS SPGSPGTPGS RSRTPSLPTP PTREPKKVAV VRTPPKSPSS AK SRLQTAP VPMPDLKNVK SKIGSTENLK HQPGGGKVQI INKKLDLSNV QSKCGSKDNI KHVPGGGSVQ IVYKPVDLSK VTS KCGSLG NIHHKPGGGQ VEVKSEKLDF KDRVQSKIGS LDNITHVPGG GNKKIETHKL TFRENAKAKT DHGAEIVYKS PVVS GDTSP RHLSNVSSTG SIDMVDSPQL ATLADEVSAS LAKQGL

UniProtKB: Microtubule-associated protein tau

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 76 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.78 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.36 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53363
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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