3WAL

Crystal structure of human LC3A_2-121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism.

Suzuki, H.Tabata, K.Morita, E.Kawasaki, M.Kato, R.Dobson, R.C.Yoshimori, T.Wakatsuki, S.

(2014) Structure 22: 47-58

  • DOI: 10.1016/j.str.2013.09.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Autophagy is a bulk degradation pathway that removes cytosolic materials to maintain cellular homeostasis. The autophagy-related gene 13 (Atg13) and microtubule associate protein 1 light chain 3 (LC3) proteins are required for autophagosome formation ...

    Autophagy is a bulk degradation pathway that removes cytosolic materials to maintain cellular homeostasis. The autophagy-related gene 13 (Atg13) and microtubule associate protein 1 light chain 3 (LC3) proteins are required for autophagosome formation. We demonstrate that each of the human LC3 isoforms (LC3A, LC3B, and LC3C) interacts with Atg13 via the LC3 interacting region (LIR) of Atg13. Using X-ray crystallography, we solved the macromolecular structures of LC3A and LC3C, along with the complex structures of the LC3 isoforms with the Atg13 LIR. Together, our structural and binding analyses reveal that the side-chain of Lys49 of LC3 acts as a gatekeeper to regulate binding of the LIR. We verified this observation by mutation of Lys49 in LC3A, which significantly reduces LC3A positive puncta formation in cultured cells. Our results suggest that specific affinity of the LC3 isoforms to the Atg13 LIR is required for proper autophagosome formation.


    Organizational Affiliation

    Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8020, New Zealand; Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan. Electronic address: hironori.suzuki@canterbury.ac.nz.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3A
A
125Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3A
Find proteins for Q9H492 (Homo sapiens)
Go to Gene View: MAP1LC3A
Go to UniProtKB:  Q9H492
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLT
Query on MLT

Download SDF File 
Download CCD File 
A
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.181 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 92.980α = 90.00
b = 92.980β = 90.00
c = 33.090γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references