8FKM | pdb_00008fkm

Human Atg3 with deletions of residues 1 to 25 and 90 to 190

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-12-21 Released: 2023-09-13 
  • Deposition Author(s): Ye, Y.S., Tian, F.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 8FKM

This is version 1.1 of the entry. See complete history

Literature

Multifaceted membrane interactions of human Atg3 promote LC3-phosphatidylethanolamine conjugation during autophagy.

Ye, Y.Tyndall, E.R.Bui, V.Bewley, M.C.Wang, G.Hong, X.Shen, Y.Flanagan, J.M.Wang, H.G.Tian, F.

(2023) Nat Commun 14: 5503-5503

  • DOI: https://doi.org/10.1038/s41467-023-41243-4
  • Primary Citation Related Structures: 
    8FKM

  • PubMed Abstract: 

    Autophagosome formation, a crucial step in macroautophagy (autophagy), requires the covalent conjugation of LC3 proteins to the amino headgroup of phosphatidylethanolamine (PE) lipids. Atg3, an E2-like enzyme, catalyzes the transfer of LC3 from LC3-Atg3 to PEs in targeted membranes. Here we show that the catalytically important C-terminal regions of human Atg3 (hAtg3) are conformationally dynamic and directly interact with the membrane, in collaboration with its N-terminal membrane curvature-sensitive helix. The functional relevance of these interactions was confirmed by in vitro conjugation and in vivo cellular assays. Therefore, highly curved phagophoric rims not only serve as a geometric cue for hAtg3 recruitment, but also their interaction with hAtg3 promotes LC3-PE conjugation by targeting its catalytic center to the membrane surface and bringing substrates into proximity. Our studies advance the notion that autophagosome biogenesis is directly guided by the spatial interactions of Atg3 with highly curved phagophoric rims.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.

Macromolecule Content 

  • Total Structure Weight: 22.09 kDa 
  • Atom Count: 1,554 
  • Modeled Residue Count: 189 
  • Deposited Residue Count: 189 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-like-conjugating enzyme ATG3189Homo sapiensMutation(s): 0 
Gene Names: ATG3APG3APG3L
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NT62 (Homo sapiens)
Explore Q9NT62 
Go to UniProtKB:  Q9NT62
PHAROS:  Q9NT62
GTEx:  ENSG00000144848 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NT62
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127730
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127954
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA222349

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references