7BRN

Crystal structure of Atg40 AIM fused to Atg8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.

Mochida, K.Yamasaki, A.Matoba, K.Kirisako, H.Noda, N.N.Nakatogawa, H.

(2020) Nat Commun 11: 3306-3306

  • DOI: https://doi.org/10.1038/s41467-020-17163-y
  • Primary Citation of Related Structures:  
    7BRN, 7BRQ, 7BRT, 7BRU

  • PubMed Abstract: 

    The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.


  • Organizational Affiliation

    School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 40,Autophagy-related protein 8134Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: ATG40YOR152CO3536ATG8APG8AUT7CVT5YBL078CYBL0732
UniProt
Find proteins for Q99325 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99325 
Go to UniProtKB:  Q99325
Find proteins for P38182 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38182 
Go to UniProtKB:  P38182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ99325P38182
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.729α = 90
b = 74.729β = 90
c = 57.092γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17K18339
Japan Society for the Promotion of Science (JSPS)Japan19H05707
Japan Science and TechnologyJapanJPMJCR13M7

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description