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- EMDB-15408: Tube assembly of Atg18-PR72AA -

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Basic information

Entry
Database: EMDB / ID: EMD-15408
TitleTube assembly of Atg18-PR72AA
Map datasharpened map from CryoSPARC software
Sample
  • Complex: Filament assembly of Atg18-PR72AA
    • Protein or peptide: Autophagy-related protein 18
Keywordsautophagy / membrane remodeling / PIP binding / PI3P / PI(3 / 5)P2 / lipid binding protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of phosphatidylinositol biosynthetic process / PAS complex / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phagophore / positive regulation of vacuole organization / vacuolar protein processing / Macroautophagy / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy ...regulation of phosphatidylinositol biosynthetic process / PAS complex / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phagophore / positive regulation of vacuole organization / vacuolar protein processing / Macroautophagy / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / late endosome to vacuole transport / pexophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / phagophore assembly site / fungal-type vacuole membrane / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / autophagosome assembly / ubiquitin binding / cell periphery / macroautophagy / protein-macromolecule adaptor activity / endosome / endosome membrane / protein-containing complex / cytosol
Similarity search - Function
: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMann D / Fromm S / Martinez-Sanchez A / Gopaldass N / Mayer A / Sachse C
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: Nat Commun / Year: 2023
Title: Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds.
Authors: Daniel Mann / Simon A Fromm / Antonio Martinez-Sanchez / Navin Gopaldass / Ramona Choy / Andreas Mayer / Carsten Sachse /
Abstract: Autophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of ...Autophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of Atg2 and Atg9 at the isolation membrane remains to be understood. Here, we determined the cryo-EM structures of Atg18 organized in helical tubes, Atg18 oligomers in solution as well as on lipid membrane scaffolds. The helical assembly is composed of Atg18 tetramers forming a lozenge cylindrical lattice with remarkable structural similarity to the COPII outer coat. When reconstituted with lipid membranes, using subtomogram averaging we determined tilted Atg18 dimer structures bridging two juxtaposed lipid membranes spaced apart by 80 Å. Moreover, lipid reconstitution experiments further delineate the contributions of Atg18's FRRG motif and the amphipathic helical extension in membrane interaction. The observed structural plasticity of Atg18's oligomeric organization and membrane binding properties provide a molecular framework for the positioning of downstream components of the autophagy machinery.
History
DepositionJul 18, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15408.png

Downloads & links

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Map

FileDownload / File: emd_15408.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from CryoSPARC software
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.0264277 - 2.4267452
Average (Standard dev.)0.026002735 (±0.1115484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15408_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: autosharpened map from Phenix software

Fileemd_15408_additional_1.map
Annotationautosharpened map from Phenix software
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_15408_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15408_half_map_2.map
Annotationhalf map B
Projections & Slices
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Histogram

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Sample components

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Entire : Filament assembly of Atg18-PR72AA

EntireName: Filament assembly of Atg18-PR72AA
Components
  • Complex: Filament assembly of Atg18-PR72AA
    • Protein or peptide: Autophagy-related protein 18

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Supramolecule #1: Filament assembly of Atg18-PR72AA

SupramoleculeName: Filament assembly of Atg18-PR72AA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Autophagy-related protein 18

MacromoleculeName: Autophagy-related protein 18 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.045777 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDSSPTINF INFNQTGTCI SLGTSKGFKI FNCEPFGKFY SEDSGGYAIV EMLFSTSLLA LVGIGDQPAL SAARLRIINT KKHSIICEV TFPTSILSVK MNKSRLVVLL QEQIYIYDIN TMRLLHTIET NPNPRGLMAM SPSVANSYLV YPSPPKVINS E IKAHATTN ...String:
MSDSSPTINF INFNQTGTCI SLGTSKGFKI FNCEPFGKFY SEDSGGYAIV EMLFSTSLLA LVGIGDQPAL SAARLRIINT KKHSIICEV TFPTSILSVK MNKSRLVVLL QEQIYIYDIN TMRLLHTIET NPNPRGLMAM SPSVANSYLV YPSPPKVINS E IKAHATTN NITLSVGGNT ETSFKRDQQD AGHSDISDLD QYSSFTKRDD ADPTSSNGGN SSIIKNGDVI VFNLETLQPT MV IEAHKGE IAAMAISFDG TLMATASDKG TIIRVFDIET GDKIYQFRRG TYATRIYSIS FSEDSQYLAV TGSSKTVHIF KLG HSMSNN KLDSDDSNME EAAADDSSLD TTSIDALSDE ENPTRLAREP YVDASRKTMG RMIRYSSQKL SRRAARTLGQ IFPI KVTSL LESSRHFASL KLPVETNSHV MTISSIGSPI DIDTSEYPEL FETGNSASTE SYHEPVMKMV PIRVVSSDGY LYNFV MDPE RGGDCLILSQ YSILMD

UniProtKB: Autophagy-related protein 18

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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: 7.2
GridModel: UltrAuFoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2380 / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
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

Final reconstructionApplied symmetry - Helical parameters - Δz: 19.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 70 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 87223
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8afq:
Tube assembly of Atg18-PR72AA

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