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- EMDB-17176: TMEM106B Fold I-d filament from Guam ALS/PDC -

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Basic information

Entry
Database: EMDB / ID: EMD-17176
TitleTMEM106B Fold I-d filament from Guam ALS/PDC
Map data
Sample
  • Complex: TMEM106B Fold1-d filaments from Guam ALS/PDC
    • Protein or peptide: Transmembrane protein 106B
KeywordsTMEM106B / Guam ALS/PDC / PROTEIN FIBRIL
Function / homology
Function and homology information


lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / dendrite morphogenesis / lysosome organization / lysosomal transport / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / dendrite morphogenesis / lysosome organization / lysosomal transport / neuron cellular homeostasis / late endosome membrane / ATPase binding / lysosome / endosome / lysosomal membrane / plasma membrane
Similarity search - Function
Transmembrane protein 106 / : / : / TM106 protein C-terminal domain / Transmembrane protein 106 N-terminal region
Similarity search - Domain/homology
Transmembrane protein 106B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsQi C / Yang S / Scheres SHW / Goedert M
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1013 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184291 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Tau filaments from amyotrophic lateral sclerosis/parkinsonism-dementia complex adopt the CTE fold.
Authors: Chao Qi / Bert M Verheijen / Yasumasa Kokubo / Yang Shi / Stephan Tetter / Alexey G Murzin / Asa Nakahara / Satoru Morimoto / Marc Vermulst / Ryogen Sasaki / Eleonora Aronica / Yoshifumi ...Authors: Chao Qi / Bert M Verheijen / Yasumasa Kokubo / Yang Shi / Stephan Tetter / Alexey G Murzin / Asa Nakahara / Satoru Morimoto / Marc Vermulst / Ryogen Sasaki / Eleonora Aronica / Yoshifumi Hirokawa / Kiyomitsu Oyanagi / Akiyoshi Kakita / Benjamin Ryskeldi-Falcon / Mari Yoshida / Masato Hasegawa / Sjors H W Scheres / Michel Goedert /
Abstract: The amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is ...The amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterized by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here, we used electron cryo-microscopy to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in three Kii cases and tau filaments with the corticobasal degeneration fold in one Kii case. We identified a new Type III CTE tau filament, where protofilaments pack against each other in an antiparallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors.
History
DepositionApr 20, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17176.png

Downloads & links

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Map

FileDownload / File: emd_17176.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.020688767 - 0.038850885
Average (Standard dev.)0.00025535398 (±0.0025705728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17176_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_17176_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17176_half_map_2.map
Projections & Slices
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Sample components

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Entire : TMEM106B Fold1-d filaments from Guam ALS/PDC

EntireName: TMEM106B Fold1-d filaments from Guam ALS/PDC
Components
  • Complex: TMEM106B Fold1-d filaments from Guam ALS/PDC
    • Protein or peptide: Transmembrane protein 106B

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Supramolecule #1: TMEM106B Fold1-d filaments from Guam ALS/PDC

SupramoleculeName: TMEM106B Fold1-d filaments from Guam ALS/PDC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transmembrane protein 106B

MacromoleculeName: Transmembrane protein 106B / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.142295 KDa
SequenceString: MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ ...String:
MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ VQFSKTVIGK ARLNNISIIG PLDMKQIDYT VPTVIAEEMS YMYDFCTLIS IKVHNIVLMM QVTVTTTYFG HS EQISQER YQYVDCGRNT TYQLGQSEYL NVLQPQQ

UniProtKB: Transmembrane protein 106B

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsTMEM106B Fold1-d filament from Guam ALS/PDC
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.79 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.42 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11131
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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