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Open data
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Basic information
Entry | Database: PDB / ID: 8afy | ||||||
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Title | Subtomogram average of membrane-bound Atg18 oligomers | ||||||
![]() | Autophagy-related protein 18 | ||||||
![]() | MEMBRANE PROTEIN / autophagy / membrane remodeling / PIP binding / PI3P / PI(3 / 5)P2 / lipid binding protein | ||||||
Function / homology | ![]() 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 / glycophagy / Macroautophagy / 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 / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / pexophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / phagophore assembly site / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / fungal-type vacuole membrane / vacuolar membrane / extrinsic component of membrane / autophagosome assembly / ubiquitin binding / cell periphery / macroautophagy / endosome membrane / endosome / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 26 Å | ||||||
![]() | Mann, D. / Fromm, S. / Martinez-Sanchez, A. / Gopaldass, N. / Mayer, A. / Sachse, C. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 610.6 KB | Display | ![]() |
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PDB format | ![]() | 475.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 71.4 KB | Display | |
Data in CIF | ![]() | 107.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15412MC ![]() 8afqC ![]() 8afwC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 55045.777 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: ATG18, AUT10, CVT18, NMR1, SVP1, YFR021W / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: Subtomogram average of membrane-bound Atg18 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 291 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
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Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 26 Å / Resolution method: OTHER / Num. of particles: 8300 / Algorithm: BACK PROJECTION / Details: Mask-less FDR-FSC at 1% FDR / Symmetry type: POINT | |||||||||||||||||||||
EM volume selection | Num. of tomograms: 16 / Num. of volumes extracted: 8300 | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Fitted 4x dimer "T" from Atg18 filament structure to interpret the density as a tetramer of dimers |