4GXL

The crystal structure of Galectin-8 C-CRD in complex with NDP52


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.023 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Sterical hindrance promotes selectivity of the autophagy cargo receptor NDP52 for the danger receptor galectin-8 in antibacterial autophagy

Li, S.Wandel, M.P.Li, F.Liu, Z.He, C.Wu, J.Shi, Y.Randow, F.

(2013) Sci.Signal. 6: ra9-ra9

  • DOI: 10.1126/scisignal.2003730

  • PubMed Abstract: 
  • Autophagy, the process of lysosome-dependent degradation of cytosolic components, is a mechanism by which cells selectively engulf invading pathogens to protect themselves against infection. Galectin-8, a cytosolic protein with specificity for β-gala ...

    Autophagy, the process of lysosome-dependent degradation of cytosolic components, is a mechanism by which cells selectively engulf invading pathogens to protect themselves against infection. Galectin-8, a cytosolic protein with specificity for β-galactoside-containing glycans, binds endosomal and lysosomal membranes that have been damaged, for example, by pathogens, and selectively recruits the autophagy cargo receptor NDP52 to induce autophagy. We solved the crystal structure of the NDP52-galectin-8 complex to show how NDP52 exclusively binds galectin-8 and, consequently, why other galectins do not restrict the growth of Salmonella in human cells.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin-8
A
153Homo 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
Peptide from Calcium-binding and coiled-coil domain-containing protein 2
B
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.023 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.087α = 90.00
b = 124.826β = 90.00
c = 43.737γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Advisory, Refinement description