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- EMDB-14174: TMEM106B filaments with Fold I from Alzheimer's disease (case 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-14174
TitleTMEM106B filaments with Fold I from Alzheimer's disease (case 1)
Map dataSharpened map of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
Sample
  • Tissue: TMEM106B
    • Protein or peptide: Transmembrane protein 106B
KeywordsAmyloid / neurodegeneration / filament / TMEM106B / 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 / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / 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: 2.64 Å
AuthorsLovestam S / Schweighauser M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nature / Year: 2022
Title: Age-dependent formation of TMEM106B amyloid filaments in human brains.
Authors: Manuel Schweighauser / Diana Arseni / Mehtap Bacioglu / Melissa Huang / Sofia Lövestam / Yang Shi / Yang Yang / Wenjuan Zhang / Abhay Kotecha / Holly J Garringer / Ruben Vidal / Grace I ...Authors: Manuel Schweighauser / Diana Arseni / Mehtap Bacioglu / Melissa Huang / Sofia Lövestam / Yang Shi / Yang Yang / Wenjuan Zhang / Abhay Kotecha / Holly J Garringer / Ruben Vidal / Grace I Hallinan / Kathy L Newell / Airi Tarutani / Shigeo Murayama / Masayuki Miyazaki / Yuko Saito / Mari Yoshida / Kazuko Hasegawa / Tammaryn Lashley / Tamas Revesz / Gabor G Kovacs / John van Swieten / Masaki Takao / Masato Hasegawa / Bernardino Ghetti / Maria Grazia Spillantini / Benjamin Ryskeldi-Falcon / Alexey G Murzin / Michel Goedert / Sjors H W Scheres /
Abstract: Many age-dependent neurodegenerative diseases, such as Alzheimer's and Parkinson's, are characterized by abundant inclusions of amyloid filaments. Filamentous inclusions of the proteins tau, amyloid- ...Many age-dependent neurodegenerative diseases, such as Alzheimer's and Parkinson's, are characterized by abundant inclusions of amyloid filaments. Filamentous inclusions of the proteins tau, amyloid-β, α-synuclein and transactive response DNA-binding protein (TARDBP; also known as TDP-43) are the most common. Here we used structure determination by cryogenic electron microscopy to show that residues 120-254 of the lysosomal type II transmembrane protein 106B (TMEM106B) also form amyloid filaments in human brains. We determined the structures of TMEM106B filaments from a number of brain regions of 22 individuals with abundant amyloid deposits, including those resulting from sporadic and inherited tauopathies, amyloid-β amyloidoses, synucleinopathies and TDP-43 proteinopathies, as well as from the frontal cortex of 3 individuals with normal neurology and no or only a few amyloid deposits. We observed three TMEM106B folds, with no clear relationships between folds and diseases. TMEM106B filaments correlated with the presence of a 29-kDa sarkosyl-insoluble fragment and globular cytoplasmic inclusions, as detected by an antibody specific to the carboxy-terminal region of TMEM106B. The identification of TMEM106B filaments in the brains of older, but not younger, individuals with normal neurology indicates that they form in an age-dependent manner.
History
DepositionJan 21, 2022-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0068
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0068
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7qvc
  • Surface level: 0.0068
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7qvc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_14174.png

Downloads & links

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Map

FileDownload / File: emd_14174.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 232.64 Å		0.73 Å/pix.
x 320 pix.
= 232.64 Å		0.73 Å/pix.
x 320 pix.
= 232.64 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: 0.0068 / Movie #1: 0.0068
Minimum - Maximum-0.011593033 - 0.025287697
Average (Standard dev.)0.00012165702 (±0.001470615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 232.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.7270.7270.727
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z232.640232.640232.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0120.0250.000

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Supplemental data

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Half map: Half map 2 of TMEM106B filaments with Fold...

Fileemd_14174_half_map_1.map
AnnotationHalf map 2 of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of TMEM106B filaments with Fold...

Fileemd_14174_half_map_2.map
AnnotationHalf map 1 of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TMEM106B

EntireName: TMEM106B
Components
  • Tissue: TMEM106B
    • Protein or peptide: Transmembrane protein 106B

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Supramolecule #1: TMEM106B

SupramoleculeName: TMEM106B / type: tissue / 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: 3 / 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: FEI FALCON IV (4k 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: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.81 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.42 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Software - details: Good stuff. / Number images used: 47414
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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