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- EMDB-76981: Supplemental: alpha-synuclein oligomers on the surface of a mitoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-76981
TitleSupplemental: alpha-synuclein oligomers on the surface of a mitochondrial membrane
Map dataalpha-syn oligomers interacting on the surface of a mitochondrial membrane
Sample
  • Organelle or cellular component: Cell lysate from 3k M17D neuroblastoma cell line
Keywordsintrinsic disorder / phase separation / neurodegeneration / membrane binding / neurotransmitter regulation / mitochondria / CHAPERONE
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / negative staining
AuthorsJaber N / Dai W
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S100D036338 United States
National Science Foundation (NSF, United States)MCB-2046180 United States
CitationJournal: EMBO Rep / Year: 2026
Title: Lipid droplets promote aberrant liquid-liquid phase separation of alpha-synuclein impairing energy homeostasis.
Authors: Jose Cevallos / Elena Eubanks / Sunghoo Jung / Yiming Huang / Elyse Guadagno / Nora Jaber / Yuzhou Xia / Jinying Wang / Huan Wang / Neeharika Rao Suvvari / Aryan Doshi / Nitya Ravinutala / ...Authors: Jose Cevallos / Elena Eubanks / Sunghoo Jung / Yiming Huang / Elyse Guadagno / Nora Jaber / Yuzhou Xia / Jinying Wang / Huan Wang / Neeharika Rao Suvvari / Aryan Doshi / Nitya Ravinutala / Alejandro Mosera / Timothy Hsu / Jiya Mody / Benjamin Sacks / Anvi Narayan / Breanna Smith / Maia Wang / Meghana Gottapu / Heba Alnakhala / Nagendran Ramalingam / Arati Tripathi / Tim Bartels / Ulf Dettmer / Zheng Shi / Wei Dai / Eleanna Kara /
Abstract: Alpha-synuclein (αSyn) inclusions are a defining neuropathological feature of Parkinson's disease, but the cellular events that initiate their formation and promote neurotoxicity remain incompletely ...Alpha-synuclein (αSyn) inclusions are a defining neuropathological feature of Parkinson's disease, but the cellular events that initiate their formation and promote neurotoxicity remain incompletely understood. Aberrant liquid-liquid phase separation has emerged as a potential early step in αSyn dysregulation, yet the physiological triggers and functional consequences of this process are unclear. Here, we show that lipid droplets promote the spontaneous phase separation of wild-type and E46K mutant αSyn into condensates. These condensates sequester lipid droplets and impair their turnover, indicating disruption of cellular lipid homeostasis. Mitochondria in close proximity to αSyn condensates exhibit reduced membrane potential and increased mitophagy. Correlative light and electron microscopy further reveals αSyn oligomers associated with mitochondrial membranes displaying structural abnormalities. Together, these findings identify lipid droplets as drivers of aberrant αSyn phase separation and suggest that lipid droplet-rich condensates contribute to mitochondrial dysfunction and impaired energy homeostasis. Given the enrichment of lipid droplets within neuromelanin-containing dopaminergic neurons of the substantia nigra, this mechanism may be relevant to the selective neuronal vulnerability observed in Parkinson's disease.
History
DepositionApr 30, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76981.png

Downloads & links

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Map

FileDownload / File: emd_76981.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationalpha-syn oligomers interacting on the surface of a mitochondrial membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.69 Å/pix.
x 256 pix.
= 3504.128 Å		13.69 Å/pix.
x 1536 pix.
= 21024.768 Å		13.69 Å/pix.
x 1152 pix.
= 15768.576 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.688 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-22.183992 - 7.618059
Average (Standard dev.)0.000000001269664 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-768-576-128
Dimensions15361152256
Spacing11521536256
CellA: 15768.576 Å / B: 21024.768 Å / C: 3504.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cell lysate from 3k M17D neuroblastoma cell line

EntireName: Cell lysate from 3k M17D neuroblastoma cell line
Components
  • Organelle or cellular component: Cell lysate from 3k M17D neuroblastoma cell line

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Supramolecule #1: Cell lysate from 3k M17D neuroblastoma cell line

SupramoleculeName: Cell lysate from 3k M17D neuroblastoma cell line / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTris-BaseTris-Base
10.0 mMNaClsodium chloride
3.0 mMMgCl2magnesium chloride
StainingType: POSITIVE / Material: MitoTracker / Details: Cells were stained with MitoTracker before lysing.
GridModel: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP / Details: Front blot time: 6 seconds.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 6 nm

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number real images: 41 / Average electron dose: 26.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 10.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 26000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: EMAN2 / Number images used: 41
CTF correctionType: NONE

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