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- EMDB-50587: TMEM106B filaments from Biondi bodies (Biondi variant) -

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Basic information

Entry
Database: EMDB / ID: EMD-50587
TitleTMEM106B filaments from Biondi bodies (Biondi variant)
Map dataPostprocessed cryo-EM map of TMEM106B fold 1 filaments extracted from Biondi bodies
Sample
  • Tissue: TMEM106B Filaments
    • Protein or peptide: Transmembrane protein 106B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTMEM106B / Amyloid / Biondi bodies / Choroid plexus / 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 / lysosomal transport / lysosome organization / 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 / lysosomal transport / lysosome organization / 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
AuthorsGhetti B / Schweighauser M / Jacobsen MH / Gray D / Bacioglu M / Murzin AG / Glazier BS / Vidal R / Newell KL / Gao S ...Ghetti B / Schweighauser M / Jacobsen MH / Gray D / Bacioglu M / Murzin AG / Glazier BS / Vidal R / Newell KL / Gao S / Garringer HJ / Spillantini MG / Scheres SHW / Goedert M
Funding support United Kingdom, United States, 5 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
National Institutes of Health/National Institute on Aging (NIH/NIA)P30-AG010133 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P30-AG072976 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01-NS110437 United States
CitationJournal: Acta Neuropathol / Year: 2024
Title: TMEM106B amyloid filaments in the Biondi bodies of ependymal cells.
Authors: Bernardino Ghetti / Manuel Schweighauser / Max H Jacobsen / Derrick Gray / Mehtap Bacioglu / Alexey G Murzin / Bradley S Glazier / Taxiarchis Katsinelos / Ruben Vidal / Kathy L Newell / ...Authors: Bernardino Ghetti / Manuel Schweighauser / Max H Jacobsen / Derrick Gray / Mehtap Bacioglu / Alexey G Murzin / Bradley S Glazier / Taxiarchis Katsinelos / Ruben Vidal / Kathy L Newell / Sujuan Gao / Holly J Garringer / Maria Grazia Spillantini / Sjors H W Scheres / Michel Goedert /
Abstract: Biondi bodies are filamentous amyloid inclusions of unknown composition in ependymal cells of the choroid plexuses, ependymal cells lining cerebral ventricles and ependymal cells of the central canal ...Biondi bodies are filamentous amyloid inclusions of unknown composition in ependymal cells of the choroid plexuses, ependymal cells lining cerebral ventricles and ependymal cells of the central canal of the spinal cord. Their formation is age-dependent and they are commonly associated with a variety of neurodegenerative conditions, including Alzheimer's disease and Lewy body disorders. Here, we show that Biondi bodies are strongly immunoreactive with TMEM239, an antibody specific for inclusions of transmembrane protein 106B (TMEM106B). Biondi bodies were labelled by both this antibody and the amyloid dye pFTAA. Many Biondi bodies were also labelled for TMEM106B and the lysosomal markers Hexosaminidase A and Cathepsin D. By transmission immuno-electron microscopy, Biondi bodies of choroid plexuses were decorated by TMEM239 and were associated with structures that resembled residual bodies or secondary lysosomes. By electron cryo-microscopy, TMEM106B filaments from Biondi bodies of choroid plexuses were similar (Biondi variant), but not identical, to the fold I that was previously identified in filaments from brain parenchyma.
History
DepositionJun 10, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50587.png

Downloads & links

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Map

FileDownload / File: emd_50587.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed cryo-EM map of TMEM106B fold 1 filaments extracted from Biondi bodies
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

Slices (1/3)

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: 0.00868
Minimum - Maximum-0.024485258 - 0.052142903
Average (Standard dev.)0.00020760878 (±0.0024007175)
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_50587_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM halfmap 1 of TMEM106B fold 1 filaments...

Fileemd_50587_half_map_1.map
AnnotationCryo-EM halfmap 1 of TMEM106B fold 1 filaments extracted from Biondi bodies
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM halfmap 2 of TMEM106B fold 1 filaments...

Fileemd_50587_half_map_2.map
AnnotationCryo-EM halfmap 2 of TMEM106B fold 1 filaments extracted from Biondi bodies
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 Filaments

EntireName: TMEM106B Filaments
Components
  • Tissue: TMEM106B Filaments
    • Protein or peptide: Transmembrane protein 106B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TMEM106B Filaments

SupramoleculeName: TMEM106B Filaments / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: TMEM106B filaments extracted from Biondi bodies of Alzheimer's disease
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: Choroid plexus

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Macromolecule #1: Transmembrane protein 106B

MacromoleculeName: Transmembrane protein 106B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.50268 KDa
SequenceString:
SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS VEVENITAQV QFSKTVIGKA RLNNITIIGP LDMKQIDYTV PTVIAEEMS YMYDFCTLIS IKVHNIVLMM QVTVTTTYFG HSEQISQERY QYVDCG

UniProtKB: Transmembrane protein 106B

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.88 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.46 °
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. 4.1) / Number images used: 38763
Segment selectionNumber selected: 685561 / Software - Name: RELION (ver. 4.1)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7qvc


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9fnb:
TMEM106B filaments from Biondi bodies (Biondi variant)

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