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- EMDB-50659: Cryo-electron tomogram of ATG2A and small unilamellar vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-50659
TitleCryo-electron tomogram of ATG2A and small unilamellar vesicles
Map dataCryo-electron tomogram of ATG2A and small unilamellar vesicles (denoised using IsoNet)
Sample
  • Complex: ATG2A and small unilamellar vesicles
Keywordsautophagy / intracellular trafficking / membranes / vesicles / LIPID TRANSPORT
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsDahmane S / Wang N / Stjepanovic G / Carlson LA
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council202101145 Sweden
Swedish Research Council201805851 Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for lipid transfer by the ATG2A-ATG9A complex.
Authors: Yang Wang / Selma Dahmane / Rujuan Ti / Xinyi Mai / Lizhe Zhu / Lars-Anders Carlson / Goran Stjepanovic /
Abstract: Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid ...Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid transfer and re-equilibration between membranes for autophagosome formation. Here we report the cryo-electron microscopy structures of human ATG2A in complex with WD-repeat protein interacting with phosphoinositides 4 (WIPI4) at 3.2 Å and the ATG2A-WIPI4-ATG9A complex at 7 Å global resolution. On the basis of molecular dynamics simulations, we propose a mechanism of lipid extraction from the donor membranes. Our analysis revealed 3:1 stoichiometry of the ATG9A-ATG2A complex, directly aligning the ATG9A lateral pore with ATG2A lipid transfer cavity, and an interaction of the ATG9A trimer with both the N-terminal and the C-terminal tip of rod-shaped ATG2A. Cryo-electron tomography of ATG2A liposome-binding states showed that ATG2A tethers lipid vesicles at different orientations. In summary, this study provides a molecular basis for the growth of the phagophore membrane and lends structural insights into spatially coupled lipid transport and re-equilibration during autophagosome formation.
History
DepositionJun 17, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50659.png

Downloads & links

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Map

FileDownload / File: emd_50659.map.gz / Format: CCP4 / Size: 306.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of ATG2A and small unilamellar vesicles (denoised using IsoNet)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.12 Å/pix.
x 141 pix.
= 1567.92 Å		11.12 Å/pix.
x 742 pix.
= 8251.04 Å		11.12 Å/pix.
x 767 pix.
= 8529.04 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: 11.12 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-6.444796 - 33.046931999999998
Average (Standard dev.)0.4702266 (±0.31675494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions742767141
Spacing767742141
CellA: 8529.04 Å / B: 8251.04 Å / C: 1567.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: un-denoised map

Fileemd_50659_additional_1.map
Annotationun-denoised 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 : ATG2A and small unilamellar vesicles

EntireName: ATG2A and small unilamellar vesicles
Components
  • Complex: ATG2A and small unilamellar vesicles

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Supramolecule #1: ATG2A and small unilamellar vesicles

SupramoleculeName: ATG2A and small unilamellar vesicles / type: complex / ID: 1 / Parent: 0 / Details: Purified human protein mixed with vesicles (SUVs).
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: CMC-Utrecht / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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