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- EMDB-33055: Cryo-EM structure of the TMEM106B fibril from Parkinson's disease... -

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Basic information

Entry
Database: EMDB / ID: EMD-33055
TitleCryo-EM structure of the TMEM106B fibril from Parkinson's disease dementia
Map data
Sample
  • Organelle or cellular component: the fibril formed by TMEM106B from Parkinson's disease dementia
    • Protein or peptide: Transmembrane protein 106B
KeywordsPROTEIN FIBRIL / amyloid
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 / lysosome organization / lysosomal transport / 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 / lysosome organization / lysosomal transport / 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: 3.0 Å
AuthorsZhao QY / Xia WC / Fan Y / Sun YP / Tao YQ / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2022
Title: Generic amyloid fibrillation of TMEM106B in patient with Parkinson's disease dementia and normal elders.
Authors: Yun Fan / Qinyue Zhao / Wencheng Xia / Youqi Tao / Wenbo Yu / Mingjia Chen / Yiqi Liu / Jue Zhao / Yan Shen / Yunpeng Sun / Chenfang Si / Shenqing Zhang / Yaoyang Zhang / Wensheng Li / Cong ...Authors: Yun Fan / Qinyue Zhao / Wencheng Xia / Youqi Tao / Wenbo Yu / Mingjia Chen / Yiqi Liu / Jue Zhao / Yan Shen / Yunpeng Sun / Chenfang Si / Shenqing Zhang / Yaoyang Zhang / Wensheng Li / Cong Liu / Jian Wang / Dan Li /
History
DepositionMar 11, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33055.png

Downloads & links

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Map

FileDownload / File: emd_33055.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å		0.83 Å/pix.
x 440 pix.
= 365.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00795
Minimum - Maximum-0.01832514 - 0.043799203
Average (Standard dev.)0.00021142013 (±0.0014833956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 365.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33055_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33055_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the fibril formed by TMEM106B from Parkinson's disease dementia

EntireName: the fibril formed by TMEM106B from Parkinson's disease dementia
Components
  • Organelle or cellular component: the fibril formed by TMEM106B from Parkinson's disease dementia
    • Protein or peptide: Transmembrane protein 106B

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Supramolecule #1: the fibril formed by TMEM106B from Parkinson's disease dementia

SupramoleculeName: the fibril formed by TMEM106B from Parkinson's disease dementia
type: organelle_or_cellular_component / 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: 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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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: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.45 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17752
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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