6A9J | pdb_00006a9j

Crystal structure of the PE-bound N-terminal domain of Atg2

• PDB DOI: https://doi.org/10.2210/pdb6A9J/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Enterobacteria phage RB59, Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-07-13 Released: 2019-03-20 
• Deposition Author(s): Osawa, T., Noda, N.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Atg2 mediates direct lipid transfer between membranes for autophagosome formation.

Osawa, T., Kotani, T., Kawaoka, T., Hirata, E., Suzuki, K., Nakatogawa, H., Ohsumi, Y., Noda, N.N.

(2019) Nat Struct Mol Biol 26: 281-288

• PubMed: 30911189 
• DOI: https://doi.org/10.1038/s41594-019-0203-4
• Primary Citation Related Structures: 
  6A9E, 6A9J


• PubMed Abstract: 
  

  A key event in autophagy is autophagosome formation, whereby the newly synthesized isolation membrane (IM) expands to form a complete autophagosome using endomembrane-derived lipids. Atg2 physically links the edge of the expanding IM with the endoplasmic reticulum (ER), a role that is essential for autophagosome formation. However, the molecular function of Atg2 during ER-IM contact remains unclear, as does the mechanism of lipid delivery to the IM. Here we show that the conserved amino-terminal region of Schizosaccharomyces pombe Atg2 includes a lipid-transfer-protein-like hydrophobic cavity that accommodates phospholipid acyl chains. Atg2 bridges highly curved liposomes, thereby facilitating efficient phospholipid transfer in vitro, a function that is inhibited by mutations that impair autophagosome formation in vivo. These results suggest that Atg2 acts as a lipid-transfer protein that supplies phospholipids for autophagosome formation.

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Organizational Affiliation: 
• Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
Life Science Data Research Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.
Collaborative Research Institute for Innovative Microbiology, University of Tokyo, Tokyo, Japan.
Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.54 kDa 
• Atom Count: 5,100 
• Modeled Residue Count: 675 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin,Autophagy-related protein 2	A, B	389	Enterobacteria phage RB59, Schizosaccharomyces pombe 972h- This entity is chimeric	Mutation(s): 3  Gene Names: e, RB59_126, atg2, mug36, SPBC31E1.01c, SPBC660.18c EC: 3.2.1.17
UniProt
Find proteins for O94649 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O94649  Go to UniProtKB:  O94649
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
UniProt Groups	P00720O94649

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEE	C [auth A], D [auth B]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.657	α = 90
b = 62.861	β = 91.89
c = 86.662	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Osawa, T., Noda, N.N.

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2019-04-10
  Changes: Data collection, Database references
• Version 1.3: 2019-04-17
  Changes: Data collection, Database references
• Version 2.0: 2021-10-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Refinement description