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

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Basic information

Entry
Database: PDB / ID: 9fnb
TitleTMEM106B filaments from Biondi bodies (Biondi variant)
ComponentsTransmembrane protein 106B
KeywordsPROTEIN FIBRIL / TMEM106B / Amyloid / Biondi bodies / Choroid plexus
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsGhetti, B. / Schweighauser, M. / Jacobsen, M.H. / Gray, D. / Bacioglu, M. / Murzin, A.G. / Glazier, B.S. / Vidal, R. / Newell, K.L. / Gao, S. ...Ghetti, B. / Schweighauser, M. / Jacobsen, M.H. / Gray, D. / Bacioglu, M. / Murzin, A.G. / Glazier, B.S. / Vidal, R. / Newell, K.L. / Gao, S. / Garringer, H.J. / Spillantini, M.G. / Scheres, S.H.W. / Goedert, M.
Funding support United Kingdom, United States, 5items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transmembrane protein 106B
A: Transmembrane protein 106B
C: Transmembrane protein 106B
D: Transmembrane protein 106B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,55020
Polymers62,0114
Non-polymers3,53916
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transmembrane protein 106B


Mass: 15502.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NUM4
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: TMEM106B Filaments / Type: TISSUE
Details: TMEM106B filaments extracted from Biondi bodies of Alzheimer's disease
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: Choroid plexus
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1700 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
12RELION4.13D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.46 ° / Axial rise/subunit: 4.88 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 685561
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38763 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 7QVC

7qvc


Accession code: 7QVC / Source name: PDB / Type: experimental model

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