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- EMDB-36043: The cryo-EM structure of Fe3+ induced alpha-syn fibril. -

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Basic information

Entry
Database: EMDB / ID: EMD-36043
TitleThe cryo-EM structure of Fe3+ induced alpha-syn fibril.
Map data
Sample
  • Tissue: The cryo-EM structure of PBB3 bound TMEM106B fibril.
    • Protein or peptide: Transmembrane protein 106B
KeywordsPROTEIN FIBRIL / amyloid
Function / homology
Function and homology information


lysosomal protein catabolic process / regulation of lysosome organization / lysosomal lumen acidification / lysosome localization / lysosomal transport / positive regulation of dendrite development / dendrite morphogenesis / lysosome organization / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / regulation of lysosome organization / lysosomal lumen acidification / lysosome localization / lysosomal transport / positive regulation of dendrite development / dendrite morphogenesis / 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: 3.0 Å
AuthorsZhao QY / Tao YQ / Yan F / Liu C / Li D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The cryo-EM structure of PBB3 bound TMEM106B fibril.
Authors: Zhao QY / Tao YQ / Fan Y / Liu C / Li D
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36043.png

Downloads & links

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Map

FileDownload / File: emd_36043.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 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: 0.0093
Minimum - Maximum-0.02605325 - 0.05362625
Average (Standard dev.)0.00043031055 (±0.002880547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36043_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_36043_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 cryo-EM structure of PBB3 bound TMEM106B fibril.

EntireName: The cryo-EM structure of PBB3 bound TMEM106B fibril.
Components
  • Tissue: The cryo-EM structure of PBB3 bound TMEM106B fibril.
    • Protein or peptide: Transmembrane protein 106B

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Supramolecule #1: The cryo-EM structure of PBB3 bound TMEM106B fibril.

SupramoleculeName: The cryo-EM structure of PBB3 bound TMEM106B fibril. / type: tissue / 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: 31.156318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ ...String:
MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ VQFSKTVIGK ARLNNITIIG PLDMKQIDYT VPTVIAEEMS YMYDFCTLIS IKVHNIVLMM QVTVTTTYFG HS EQISQER YQYVDCGRNT TYQLGQSEYL NVLQPQQ

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: 7.5
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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.84 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.69 °
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: 14665
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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