8KBY | pdb_00008kby

Cryo-EM structure of ATG2A

• PDB DOI: https://doi.org/10.2210/pdb8KBY/pdb
• EM Map EMD-37087: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-08-04 Released: 2024-08-07 
• Deposition Author(s): Wang, Y., Stjepanovic, G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for lipid transfer by the ATG2A-ATG9A complex.

Wang, Y., Dahmane, S., Ti, R., Mai, X., Zhu, L., Carlson, L.A., Stjepanovic, G.

(2025) Nat Struct Mol Biol 32: 35-47

• PubMed: 39174844 
• DOI: https://doi.org/10.1038/s41594-024-01376-6
• Primary Citation Related Structures: 
  8KBX, 8KBY, 8KBZ, 8KC3, 8Y1L


• PubMed Abstract: 
  

  Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid transfer and re-equilibration between membranes for autophagosome formation. Here we report the cryo-electron microscopy structures of human ATG2A in complex with WD-repeat protein interacting with phosphoinositides 4 (WIPI4) at 3.2 Å and the ATG2A-WIPI4-ATG9A complex at 7 Å global resolution. On the basis of molecular dynamics simulations, we propose a mechanism of lipid extraction from the donor membranes. Our analysis revealed 3:1 stoichiometry of the ATG9A-ATG2A complex, directly aligning the ATG9A lateral pore with ATG2A lipid transfer cavity, and an interaction of the ATG9A trimer with both the N-terminal and the C-terminal tip of rod-shaped ATG2A. Cryo-electron tomography of ATG2A liposome-binding states showed that ATG2A tethers lipid vesicles at different orientations. In summary, this study provides a molecular basis for the growth of the phagophore membrane and lends structural insights into spatially coupled lipid transport and re-equilibration during autophagosome formation.

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Organizational Affiliation: 
• Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China. [e-mail].
School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China. [e-mail].
Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden. [e-mail].
Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden. [e-mail].
Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden. [e-mail].
Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden. [e-mail].
Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 213.1 kDa 
• Atom Count: 5,050 
• Modeled Residue Count: 830 
• Deposited Residue Count: 1,938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 2 homolog A	A [auth B]	1,938	Homo sapiens	Mutation(s): 0  Gene Names: ATG2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q2TAZ0 (Homo sapiens) Explore Q2TAZ0  Go to UniProtKB:  Q2TAZ0
PHAROS:  Q2TAZ0 GTEx:  ENSG00000110046

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Wang, Y., Stjepanovic, G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31950410540
Ministry of Science and Technology (MoST, China)	China	QN2021032004L

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Data collection, Database references
• Version 1.2: 2025-01-29
  Changes: Data collection, Database references, Structure summary