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- EMDB-42294: Structure of recombinantly assembled murine alpha-synuclein fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-42294
TitleStructure of recombinantly assembled murine alpha-synuclein fibrils
Map data
Sample
  • Complex: alpha-synuclein
    • Protein or peptide: Alpha-synuclein
Keywordssynuclein / Parkinson's disease / neurodegeneration / amyloid / fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


PKR-mediated signaling / regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / platelet alpha granule membrane / membrane organization / neurotransmitter secretion / synaptic transmission, dopaminergic / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission ...PKR-mediated signaling / regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / platelet alpha granule membrane / membrane organization / neurotransmitter secretion / synaptic transmission, dopaminergic / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / nuclear outer membrane / 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 / response to iron(II) ion / regulation of reactive oxygen species metabolic process / arachidonate binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein complex oligomerization / negative regulation of thrombin-activated receptor signaling pathway / beta-tubulin binding / dopamine metabolic process / cuprous ion binding / response to type II interferon / regulation of neuronal synaptic plasticity / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / phospholipase binding / behavioral response to cocaine / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / positive regulation of synaptic transmission / phospholipid metabolic process / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / response to interleukin-1 / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / negative regulation of protein phosphorylation / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / cytoplasmic vesicle membrane / tau protein binding / terminal bouton / receptor internalization / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / presynapse / actin binding / cellular response to oxidative stress / histone binding / cell cortex / growth cone / microtubule binding / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / postsynapse / response to lipopolysaccharide / mitochondrial inner membrane
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhou Y / Sokratian A
Funding support United States, 1 items
OrganizationGrant numberCountry
Michael J. Fox FoundationASAP-020527 United States
CitationJournal: To Be Published
Title: Cryo-EM structure and characterization of recombinantly assembled murine alpha-synuclein fibrils
Authors: Zhou Y / Sokratian A
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42294.png

Downloads & links

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Map

FileDownload / File: emd_42294.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 128 pix.
= 138.24 Å		1.08 Å/pix.
x 128 pix.
= 138.24 Å		1.08 Å/pix.
x 128 pix.
= 138.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0146
Minimum - Maximum-0.053710554 - 0.08037511
Average (Standard dev.)0.00011187801 (±0.0037834584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 138.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42294_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_42294_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 : alpha-synuclein

EntireName: alpha-synuclein
Components
  • Complex: alpha-synuclein
    • Protein or peptide: Alpha-synuclein

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Supramolecule #1: alpha-synuclein

SupramoleculeName: alpha-synuclein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Alpha-synuclein

MacromoleculeName: Alpha-synuclein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.501185 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDVFMKGLSK AKEGVVAAAE KTKQGVAEAA GKTKEGVLYV GSKTKEGVVH GVTTVAEKTK EQVTNVGGAV VTGVTAVAQK TVEGAGNIA AATGFVKKDQ MGKGEEGYPQ EGILEDMPVD PGSEAYEMPS EEGYQDYEPE A

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

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Chloride
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Sodium Phosphate Dibasic
1.8 mMKH2PO4Potassium Phosphate Monobasic

Details: Phosphate-buffered saline (PBS)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 75 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
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: -0.84 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27523
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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