5XAE

mutNLIR_LC3B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.996 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel conformation of the LC3-interacting region motif revealed by the structure of a complex between LC3B and RavZ

Kwon, D.H.Kim, L.Kim, B.W.Kim, J.H.Roh, K.H.Choi, E.J.Song, H.K.

(2017) Biochem. Biophys. Res. Commun. 490: 1093-1099

  • DOI: 10.1016/j.bbrc.2017.06.173
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LC3-family member proteins play a critical role in autophagy, a cellular process responsible for the degradation of massive cellular components including intracellular pathogens. A variety of molecules involved in the autophagic pathway engage in spe ...

    LC3-family member proteins play a critical role in autophagy, a cellular process responsible for the degradation of massive cellular components including intracellular pathogens. A variety of molecules involved in the autophagic pathway engage in specific interactions with a unique sequence motif referred to as the LIR (LC3-interacting region) motif. Although identification of conserved structural features of LIR motifs in complex with LC3-family members has established a canonical LIR motif, atypical conformations of LIR motifs have recently been revealed. Here, we determined the three-dimensional crystal structures of LC3B in complex with three different LIR motifs of RavZ from Legionella pneumophila, an intracellular pathogen that can manipulate the host autophagy system. The tandem LIR motifs located in the N-terminal region of RavZ adopt a novel β-sheet conformation and thus provide specific ionic interactions with LC3B in addition to canonical hydrophobic plugged-in interactions. Consequently, these motifs possess higher binding affinity to LC3-family members than canonical LIR motifs, although the tandem repeats can only bind to one LC3 molecule. These findings broaden our understanding of the functional repertoire of LIR motifs in autophagy.


    Organizational Affiliation

    Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3B
A, B, C, D
142Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3B (MAP1ALC3)
Find proteins for Q9GZQ8 (Homo sapiens)
Go to Gene View: MAP1LC3B
Go to UniProtKB:  Q9GZQ8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.996 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.720α = 77.15
b = 53.447β = 73.18
c = 61.584γ = 85.05
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Database references