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- EMDB-76983: Supplemental: mitochondria not associated with alpha-synuclein -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76983
TitleSupplemental: mitochondria not associated with alpha-synuclein
Map datacontrol mitochondria and alpha-syn
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: To Be Published
Title: Lipid droplets promote the aberrant liquid-liquid phase separation of alpha-synuclein leading to impaired energy homeostasis
Authors: Cevallos J / Eubanks E / Jung S / Huang Y / Guadagno E / Jaber N / Xia Y / Wang J / Wang H / Suvvari NR / Doshi A / Ravinutala N / Mosera A / Hsu T / Mody J / Sacks B / Narayan A / Smith B / ...Authors: Cevallos J / Eubanks E / Jung S / Huang Y / Guadagno E / Jaber N / Xia Y / Wang J / Wang H / Suvvari NR / Doshi A / Ravinutala N / Mosera A / Hsu T / Mody J / Sacks B / Narayan A / Smith B / Wang M / Gottapu M / Ramalingam N / Tripathi A / Bartels T / Dettmer U / Shi Z / Dai W / Kara E
History
DepositionApr 30, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76983.png

Downloads & links

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Map

FileDownload / File: emd_76983.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcontrol mitochondria and alpha-syn
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 1512 pix.
= 20696.256 Å		13.69 Å/pix.
x 1120 pix.
= 15330.56 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-7.6710286 - 27.069379999999999
Average (Standard dev.)0.00000001327226 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-756-560-128
Dimensions15121120256
Spacing11201512256
CellA: 15330.56 Å / B: 20696.256 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 / Mesh: 100 / 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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