1UGM

Crystal Structure of LC3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8

Sugawara, K.Suzuki, N.N.Fujioka, Y.Mizushima, N.Ohsumi, Y.Inagaki, F.

(2004) Genes Cells 9: 611-618

  • DOI: 10.1111/j.1356-9597.2004.00750.x
  • Primary Citation of Related Structures:  
    1UGM

  • PubMed Abstract: 
  • Microtubule-associated protein light chain 3 (LC3), a mammalian homologue of yeast Atg8, plays an essential role in autophagy, which is involved in the bulk degradation of cytoplasmic components by the lysosomal system. Here, we report the crystal structure of LC3 at 2 ...

    Microtubule-associated protein light chain 3 (LC3), a mammalian homologue of yeast Atg8, plays an essential role in autophagy, which is involved in the bulk degradation of cytoplasmic components by the lysosomal system. Here, we report the crystal structure of LC3 at 2.05 A resolution with an R-factor of 21.8% and a free R-factor of 24.9%. The structure of LC3, which is similar to those of Golgi-associated ATPase enhancer of 16 kDa (GATE-16) and GABAA receptor-associated protein (GABARAP), contains a ubiquitin core with two alpha helices, alpha1 and alpha2, attached at its N-terminus. Some common and distinct features are observed among these proteins, including the conservation of residues required to form an interaction among alpha1, alpha2 and the ubiquitin core. However, the electrostatic potential surfaces of these helices differ, implicating particular roles to select specific binding partners. Hydrophobic patches on the ubiquitin core of LC3, GABARAP and GATE-16 are well conserved and are similar to the E1 binding surface of ubiquitin and NEDD8. Therefore, we propose that the hydrophobic patch is a binding surface for mammalian Atg7 similar to a ubiquitin-like conjugation system. We also propose the functional implications of the ubiquitin fold as a recognition module of target proteins.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of LC3-I
      Sugawara, K., Suzuki, N.N., Fujioka, Y., Mizushima, N., Ohsumi, Y., Inagaki, F.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1464

    Organizational Affiliation

    Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3A125Rattus norvegicusMutation(s): 0 
Gene Names: Map1lc3bMap1alc3Map1lc3
Find proteins for Q62625 (Rattus norvegicus)
Explore Q62625 
Go to UniProtKB:  Q62625
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.78α = 90
b = 60.78β = 90
c = 35.395γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance