5XAD

NLIR - LC3B fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    5XAC, 5XAD, 5XAE

  • 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 specific interactions with a unique sequence motif referred to as the LIR (LC3-interacting region) motif ...

    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. Electronic address: hksong@korea.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3BA, B119Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3BMAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ8 (Homo sapiens)
Explore Q9GZQ8 
Go to UniProtKB:  Q9GZQ8
PHAROS:  Q9GZQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZQ8
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterised proteinC, D25Legionella pneumophila subsp. pneumophilaMutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for Q5ZUV9 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZUV9 
Go to UniProtKB:  Q5ZUV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZUV9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.735α = 90
b = 65.735β = 90
c = 127.042γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Source and taxonomy