7D0I

Cryo-EM structure of Schizosaccharomyces pombe Atg9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.

Matoba, K.Kotani, T.Tsutsumi, A.Tsuji, T.Mori, T.Noshiro, D.Sugita, Y.Nomura, N.Iwata, S.Ohsumi, Y.Fujimoto, T.Nakatogawa, H.Kikkawa, M.Noda, N.N.

(2020) Nat Struct Mol Biol 27: 1185-1193

  • DOI: https://doi.org/10.1038/s41594-020-00518-w
  • Primary Citation of Related Structures:  
    7D0I

  • PubMed Abstract: 

    The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro. Cryo-EM of fission yeast Atg9 reveals a homotrimer, with two connected pores forming a path between the two membrane leaflets: one pore, located at a protomer, opens laterally to the cytoplasmic leaflet; the other, at the trimer center, traverses the membrane vertically. Mutation of residues lining the pores impaired IM expansion and autophagy activity in yeast and abolished Atg9's ability to transport phospholipids between liposome leaflets. These results suggest that phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, thereby driving autophagosomal membrane expansion.


  • Organizational Affiliation

    Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 9710Schizosaccharomyces pombe 972h-Mutation(s): 1 
Gene Names: atg9apg9SPBC15D4.07c
Membrane Entity: Yes 
UniProt
Find proteins for O74312 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74312 
Go to UniProtKB:  O74312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74312
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMN (Subject of Investigation/LOI)
Query on LMN

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth D]
J [auth D]
K [auth F]
G [auth B],
H [auth B],
I [auth D],
J [auth D],
K [auth F],
L [auth F],
M [auth H],
N [auth H],
O [auth J],
P [auth J],
Q [auth L],
R [auth L]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K06097
Japan Society for the Promotion of Science (JSPS)Japan15K21608
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101001 (support number 0053)
Japan Science and TechnologyJapanJPMJCR13M7
Japan Science and TechnologyJapanJPMJCR14M1
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101079 (support number 0739)
Japan Society for the Promotion of Science (JSPS)Japan25111004
Japan Society for the Promotion of Science (JSPS)Japan18H03989
Japan Society for the Promotion of Science (JSPS)Japan19H05707

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references