4HAN

Crystal structure of Galectin 8 with NDP52 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8.

Kim, B.W.Hong, S.B.Kim, J.H.Kwon, D.H.Song, H.K.

(2013) Nat Commun 4: 1613-1613

  • DOI: https://doi.org/10.1038/ncomms2606
  • Primary Citation of Related Structures:  
    4HAN

  • PubMed Abstract: 

    Infectious bacteria are cleared from mammalian cells by host autophagy in combination with other upstream cellular components, such as the autophagic receptor NDP52 and sugar receptor galectin-8. However, the detailed molecular basis of the interaction between these two receptors remains to be elucidated. Here, we report the biochemical characterization of both NDP52 and galectin-8 as well as the crystal structure of galectin-8 complexed with an NDP52 peptide. The unexpected observation of nicotinamide adenine dinucleotide located at the carbohydrate-binding site expands our knowledge of the sugar-binding specificity of galectin-8. The NDP52-galectin-8 complex structure explains the key determinants for recognition on both receptors and defines a special orientation of N- and C-terminal carbohydrate recognition domains of galectin-8. Dimeric NDP52 forms a ternary complex with two monomeric galectin-8 molecules as well as two LC3C molecules. These results lay the groundwork for understanding how host cells target bacterial pathogens for autophagy.


  • Organizational Affiliation

    Division of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-8
A, B
293Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
PHAROS:  O00214
GTEx:  ENSG00000116977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00214
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-binding and coiled-coil domain-containing protein 2
C, D
14Homo sapiensMutation(s): 0 
Gene Names: CALCOCO2NDP52
UniProt & NIH Common Fund Data Resources
Find proteins for Q13137 (Homo sapiens)
Explore Q13137 
Go to UniProtKB:  Q13137
PHAROS:  Q13137
GTEx:  ENSG00000136436 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13137
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.884α = 90
b = 71.884β = 90
c = 314.493γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Source and taxonomy
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations