8AFQ | pdb_00008afq

Tube assembly of Atg18-PR72AA

• PDB DOI: https://doi.org/10.2210/pdb8AFQ/pdb
• EM Map EMD-15408: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-07-18 Released: 2023-11-01 
• Deposition Author(s): Mann, D., Fromm, S., Martinez-Sanchez, A., Gopaldass, N., Mayer, A., Sachse, C.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds.

Mann, D., Fromm, S.A., Martinez-Sanchez, A., Gopaldass, N., Choy, R., Mayer, A., Sachse, C.

(2023) Nat Commun 14: 8086-8086

• PubMed: 38057304 
• DOI: https://doi.org/10.1038/s41467-023-43460-3
• Primary Citation Related Structures: 
  8AFQ, 8AFW, 8AFX, 8AFY


• PubMed 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 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.

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Organizational Affiliation: 
• Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany.
Department of Information and Communications Engineering, Faculty of Computers Sciences, University of Murcia, Murcia, Spain.
Department of Biochemistry, University of Lausanne, Epalinges, Switzerland.
Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany. [e-mail].
Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany. [e-mail].
Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 80-mer - A80 

Biological assembly 1 generated by UCSF CHIMERA 1.15_b42258. (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 220.18 kDa 
• Atom Count: 10,139 
• Modeled Residue Count: 1,304 
• Deposited Residue Count: 2,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 18	A, B [auth C], C [auth D], D [auth E]	500	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: ATG18, AUT10, CVT18, NMR1, SVP1, YFR021W
UniProt
Find proteins for P43601 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43601  Go to UniProtKB:  P43601

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Mann, D., Fromm, S., Martinez-Sanchez, A., Gopaldass, N., Mayer, A., Sachse, C.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Database references