4GXL | pdb_00004gxl

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

• PDB DOI: https://doi.org/10.2210/pdb4GXL/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-04 Released: 2013-05-08 
• Deposition Author(s): Li, S., Wandel, M.P., Li, F., Liu, Z., He, C., Wu, J., Shi, Y., Randow, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

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

• PubMed: 23386746 
• DOI: https://doi.org/10.1126/scisignal.2003730
• Primary Citation Related Structures: 
  4GXL


• 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-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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.23 kDa 
• Atom Count: 1,374 
• Modeled Residue Count: 154 
• Deposited Residue Count: 167 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-8	A	153	Homo sapiens	Mutation(s): 0  Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens) Explore O00214  Go to UniProtKB:  O00214
PHAROS:  O00214 GTEx:  ENSG00000116977

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Calcium-binding and coiled-coil domain-containing protein 2	B	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13137 (Homo sapiens) Explore Q13137  Go to UniProtKB:  Q13137
PHAROS:  Q13137 GTEx:  ENSG00000136436

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.087	α = 90
b = 124.826	β = 90
c = 43.737	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Li, S., Wandel, M.P., Li, F., Liu, Z., He, C., Wu, J., Shi, Y., Randow, F.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.2: 2024-03-20
  Changes: Advisory, Data collection, Database references, Derived calculations