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- PDB-7qvc: TMEM106B filaments with Fold I from Alzheimer's disease (case 1) -

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Basic information

Entry
Database: PDB / ID: 7qvc
TitleTMEM106B filaments with Fold I from Alzheimer's disease (case 1)
ComponentsTransmembrane protein 106BTransmembrane protein
KeywordsPROTEIN FIBRIL / Amyloid / neurodegeneration / filament / TMEM106B
Function / homology
Function and homology information


lysosomal protein catabolic process / regulation of lysosome organization / lysosomal lumen acidification / lysosome localization / positive regulation of dendrite development / dendrite morphogenesis / lysosomal transport / lysosome organization / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / regulation of lysosome organization / lysosomal lumen acidification / 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 N-terminal region / Transmembrane protein 106 / TM106 protein C-terminal domain
Similarity search - Domain/homology
Transmembrane protein 106B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLovestam, S. / Schweighauser, M. / Scheres, S.H.W.
Funding support United Kingdom, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Transmembrane protein 106B
B: Transmembrane protein 106B
C: Transmembrane protein 106B


Theoretical massNumber of molelcules
Total (without water)93,4273
Polymers93,4273
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Transmembrane protein 106B / Transmembrane protein


Mass: 31142.295 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NUM4
Has ligand of interestN

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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 / Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
2RELION4image acquisitionIt's a good programme, thanks Sjors!
13RELION43D reconstructionGood stuff.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.42 ° / Axial rise/subunit: 4.81 Å / Axial symmetry: C1
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47414 / Symmetry type: HELICAL

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