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- EMDB-15411: Single particle structure of Atg18-WT -

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Basic information

Entry
Database: EMDB / ID: EMD-15411
TitleSingle particle structure of Atg18-WT
Map datasharp map from CryoSPARC softwarew
Sample
  • Complex: Atg18
    • 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 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) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15411.png

Downloads & links

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Map

FileDownload / File: emd_15411.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map from CryoSPARC softwarew
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.758 Å		0.84 Å/pix.
x 256 pix.
= 214.758 Å		0.84 Å/pix.
x 256 pix.
= 214.758 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.76017296 - 1.1590412
Average (Standard dev.)-0.00026885155 (±0.019410064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.7584 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15411_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_15411_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15411_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Atg18

EntireName: Atg18
Components
  • Complex: Atg18
    • Protein or peptide: Autophagy-related protein 18

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Supramolecule #1: Atg18

SupramoleculeName: Atg18 / 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.62241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SPTINFINFN QTGTCISLGT SKGFKIFNCE PFGKFYSEDS GGYAIVEMLF STSLLALVGI GDQPALSPRR LRIINTKKHS IICEVTFPT SILSVKMNKS RLVVLLQEQI YIYDINTMRL LHTIETNPNP RGLMAMSPSV ANSYLVYPSP PKVINSEIKA H ATTNNITL ...String:
SPTINFINFN QTGTCISLGT SKGFKIFNCE PFGKFYSEDS GGYAIVEMLF STSLLALVGI GDQPALSPRR LRIINTKKHS IICEVTFPT SILSVKMNKS RLVVLLQEQI YIYDINTMRL LHTIETNPNP RGLMAMSPSV ANSYLVYPSP PKVINSEIKA H ATTNNITL SVGGNTETSF KRDQQDAGHS DISDLDQYSS FTKRDDADPT SSNGGNSSII KNGDVIVFNL ETLQPTMVIE AH KGEIAAM AISFDGTLMA TASDKGTIIR VFDIETGDKI YQFRRGTYAT RIYSISFSED SQYLAVTGSS KTVHIFKLGH SMS NNKLDS DDSNMEEAAA DDSSLDTTSI DALSDEENPT RLAREPYVDA SRKTMGRMIR YSSQKLSRRA ARTLGQIFPI KVTS LLESS RHFASLKLPV ETNSHVMTIS SIGSPIDIDT SEYPELFETG NSASTESYHE PVMKMVPIRV VSSDGYLYNF VMDPE RGGD CLILSQYSIL M

UniProtKB: Autophagy-related protein 18

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number real images: 5117 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 124369
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6kyb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8afx:
Single particle structure of Atg18-WT

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