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- EMDB-54402: Structure of in-vivo formed alpha-synuclein fibrils purified from... -

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Basic information

Entry
Database: EMDB / ID: EMD-54402
TitleStructure of in-vivo formed alpha-synuclein fibrils purified from a M83+/- mouse brain injected with recombinant 1B fibrils
Map dataPostprocessed EM map
Sample
  • Complex: Alpha-synuclein fibril purified from the brain of a 1B-injected M83+/- mouse
    • Protein or peptide: Alpha-synuclein
KeywordsAlpha-synuclein / Prion-like / Fibril / Paired helical filament / PROTEIN FIBRIL
Function / homology
Function and homology information


PKR-mediated signaling / regulation of neurotransmitter secretion / platelet alpha granule membrane / membrane organization / synaptic transmission, dopaminergic / neurotransmitter secretion / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake ...PKR-mediated signaling / regulation of neurotransmitter secretion / platelet alpha granule membrane / membrane organization / synaptic transmission, dopaminergic / neurotransmitter secretion / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / arachidonate binding / SNARE complex assembly / regulation of reactive oxygen species metabolic process / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / response to iron(II) ion / positive regulation of inositol phosphate biosynthetic process / regulation of locomotion / negative regulation of dopamine metabolic process / regulation of macrophage activation / synaptic vesicle priming / transporter regulator activity / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / mitochondrial ATP synthesis coupled electron transport / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / dopamine metabolic process / cuprous ion binding / protein complex oligomerization / nuclear outer membrane / positive regulation of exocytosis / response to magnesium ion / positive regulation of endocytosis / kinesin binding / synaptic vesicle endocytosis / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / regulation of neuronal synaptic plasticity / regulation of presynapse assembly / response to type II interferon / alpha-tubulin binding / positive regulation of synaptic transmission / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / cellular response to copper ion / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / axon terminus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / excitatory postsynaptic potential / phosphoprotein binding / protein tetramerization / fatty acid metabolic process / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / actin cytoskeleton / actin binding / growth cone / cellular response to oxidative stress / cell cortex / neuron apoptotic process / response to lipopolysaccharide / microtubule binding / chemical synaptic transmission / histone binding / negative regulation of neuron apoptotic process / mitochondrial outer membrane / cytoskeleton / oxidoreductase activity / postsynapse
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
Authorsvan den Heuvel L / Burger D / Kashyrina M / de La Seigliere H / Lewis AJ / De Nuccio F / Mohammed I / Verchere J / Feuillie C / Berbon M ...van den Heuvel L / Burger D / Kashyrina M / de La Seigliere H / Lewis AJ / De Nuccio F / Mohammed I / Verchere J / Feuillie C / Berbon M / Arotcarena M / Retailleau A / Bezard E / Canron M / Meissner WG / Loquet A / Bousset L / Poujol C / Nilsson KPR / Laferriere F / Baron T / Lofrumento DD / De Giorgi F / Stahlberg H / Ichas F
Funding support Switzerland, France, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationIC00I0L-231578 Switzerland
Agence Nationale de la Recherche (ANR)ANR-24-CE93-0003 France
CitationJournal: To Be Published / Year: 2024
Title: Synthetic alpha-synuclein fibrils replicate in mice causing MSA neuropathology
Authors: Burger D / Kashyrina M / van den Heuvel L / de La Seigliere H / Lewis AJ / De Nuccio F / Mohammed I / Verchere J / Feuillie C / Berbon M / Arotcarena M / Retailleau A / Bezard E / Canron M / ...Authors: Burger D / Kashyrina M / van den Heuvel L / de La Seigliere H / Lewis AJ / De Nuccio F / Mohammed I / Verchere J / Feuillie C / Berbon M / Arotcarena M / Retailleau A / Bezard E / Canron M / Meissner WG / Loquet A / Bousset L / Poujol C / Nilsson KPR / Laferriere F / Baron T / Lofrumento DD / De Giorgi F / Stahlberg H / Ichas F
History
DepositionJul 15, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54402.png

Downloads & links

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Map

FileDownload / File: emd_54402.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 400 pix.
= 585.6 Å		1.46 Å/pix.
x 400 pix.
= 585.6 Å		1.46 Å/pix.
x 400 pix.
= 585.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.075218976 - 0.11792008
Average (Standard dev.)0.000037732378 (±0.0012426373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 585.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54402_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Helically symmetrized EM map

Fileemd_54402_additional_1.map
AnnotationHelically symmetrized EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of refinement (unfiltered)

Fileemd_54402_half_map_1.map
AnnotationHalf map 2 of refinement (unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of refinement (unfiltered)

Fileemd_54402_half_map_2.map
AnnotationHalf map 1 of refinement (unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Alpha-synuclein fibril purified from the brain of a 1B-injected M...

EntireName: Alpha-synuclein fibril purified from the brain of a 1B-injected M83+/- mouse
Components
  • Complex: Alpha-synuclein fibril purified from the brain of a 1B-injected M83+/- mouse
    • Protein or peptide: Alpha-synuclein

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Supramolecule #1: Alpha-synuclein fibril purified from the brain of a 1B-injected M...

SupramoleculeName: Alpha-synuclein fibril purified from the brain of a 1B-injected M83+/- mouse
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse) / Strain: Hemizygous A53T alpha-synuclein transgenic line M83 / Organ: Brain
Molecular weightTheoretical: 14 kDa/nm

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Macromolecule #1: Alpha-synuclein

MacromoleculeName: Alpha-synuclein / type: protein_or_peptide / ID: 1 / Details: A53T / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: Hemizygous A53T alpha-synuclein transgenic line M83 / Organ: Brain
Molecular weightTheoretical: 6.037906 KDa
SequenceString:
VLYVGSKTKE GVVHGVTTVA EKTKEQVTNV GGAVVTGVTA VAQKTVEGAG SIAAATGFVK K

UniProtKB: Alpha-synuclein

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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
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris-HClTris-HCl

Details: 50 mM Tris-HCl, 150 mM NaCl, pH7.4
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY ARRAY / Support film - #0 - Film thickness: 12 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 5 / Details: The grids were not glow-discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
DetailsSarkosyl-insoluble fraction

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 42812 / Average exposure time: 3.04 sec. / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie-mode with a total of 936 frames per movie.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsA total of 40 movies was selected for manual picking
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.55 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 1913
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 3556
Software:
Namedetails
RELION (ver. 4.0.0)Used for manual picking and helical reconstruction
cryoSPARC (ver. 4.7.0)Used for selection of micrographs

Details: Particles selected by manual picking of fibril start and end points
Startup modelType of model: INSILICO MODEL
In silico model: Initial model was generated with relion_helix_inimodel2d
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9euu

chain_id: A, source_name: PDB, initial_model_type: experimental model

9euu

chain_id: B, source_name: PDB, initial_model_type: experimental model
DetailsA rigid-body fit was done using ChimeraX and a subsequent jiggle fit and all-atom refinement was done in Coot.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9rzf:
Structure of in-vivo formed alpha-synuclein fibrils purified from a M83+/- mouse brain injected with recombinant 1B fibrils

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