9FNB | pdb_00009fnb

TMEM106B filaments from Biondi bodies (Biondi variant)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

TMEM106B amyloid filaments in the Biondi bodies of ependymal cells.

Ghetti, B.Schweighauser, M.Jacobsen, M.H.Gray, D.Bacioglu, M.Murzin, A.G.Glazier, B.S.Katsinelos, T.Vidal, R.Newell, K.L.Gao, S.Garringer, H.J.Spillantini, M.G.Scheres, S.H.W.Goedert, M.

(2024) Acta Neuropathol 148: 60-60

  • DOI: https://doi.org/10.1007/s00401-024-02807-w
  • Primary Citation of Related Structures:  
    9FNB

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, USA. bghetti@iu.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein 106BA [auth B],
B [auth A],
C,
D
135Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUM4 (Homo sapiens)
Explore Q9NUM4 
Go to UniProtKB:  Q9NUM4
PHAROS:  Q9NUM4
GTEx:  ENSG00000106460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NUM4
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q9NUM4-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
H [auth B]
I [auth A]
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.1
MODEL REFINEMENTServalcat

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A025-1013
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105184291
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesP30-AG010133
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesP30-AG072976
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01-NS110437

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release