4HAN

Crystal structure of Galectin 8 with NDP52 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.551 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/ncomms2606

  • 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 interacti ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-8
A, B
293Homo sapiensMutation(s): 0 
Gene Names: LGALS8
Find proteins for O00214 (Homo sapiens)
Go to Gene View: LGALS8
Go to UniProtKB:  O00214
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calcium-binding and coiled-coil domain-containing protein 2
C, D
14Homo sapiensMutation(s): 0 
Gene Names: CALCOCO2 (NDP52)
Find proteins for Q13137 (Homo sapiens)
Go to Gene View: CALCOCO2
Go to UniProtKB:  Q13137
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.551 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 71.884α = 90.00
b = 71.884β = 90.00
c = 314.493γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Source and taxonomy