9KH4 | pdb_00009kh4

Crystal structure of Galectin-8 N-CRD with N-acetyllactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Galectin-8 binding to alpha-1 antitrypsin is a physiological mechanism in healthy individuals but exacerbates the symptoms of alpha-1 antitrypsin deficiency.

Sayed, H.Mayo, K.H.Zhou, Y.Tai, G.Su, J.

(2025) Arch Biochem Biophys 772: 110577-110577

  • DOI: https://doi.org/10.1016/j.abb.2025.110577
  • Primary Citation Related Structures: 
    9KH4

  • PubMed Abstract: 

    Alpha-1 Antitrypsin (AAT) is a serine protease inhibitor that protects lung tissue by neutralizing neutrophil elastase. Galectin-8 (Gal-8) is a tandem-repeat galectin with N- and C-terminal carbohydrate recognition domains (CRDs) that bind β-galactoside-containing N-glycans. Both proteins co-localize in pulmonary and circulatory systems, suggesting a physiological interaction. Here, we demonstrate a glycan-dependent binding between Gal-8 and AAT using pull-down assays, mass spectrometry, isothermal titration calorimetry, and size-exclusion chromatography. Importantly, binding of Gal-8 impairs AAT's protease inhibitory activity, with the N-terminal CRD of Gal-8 sufficient to disrupt AAT function. Kinetic analyses show that Gal-8 inhibits AAT and enhances trypsin activity, as evidenced by a decrease in K m and an increase in catalytic efficiency (k cat /K m ). In cell assays, Gal-8 restored trypsin-mediated proteolysis and induced cell detachment in HeLa and CHO cells despite AAT presence, confirming biological relevance. Leveraging this interaction, we developed a lactose-mediated elution method to purify AAT from human and bovine serum using Gal-8 immobilized on Ni-NTA beads. Moreover, a stable CHO cell line expressing recombinant AAT (∼2 g/L) exhibited glycosylation comparable to serum AAT and retained Gal-8 binding. Our findings reveal Gal-8 as a novel modulator of AAT activity and present a glycan-specific strategy for AAT purification, with implications for biotherapeutic production and quality control.


  • Organizational Affiliation
    • Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China.

Macromolecule Content 

  • Total Structure Weight: 17.46 kDa 
  • Atom Count: 1,426 
  • Modeled Residue Count: 150 
  • Deposited Residue Count: 150 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galectin-8150Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00214
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RNQ
(Subject of Investigation/LOI)

Query on RNQ



Download:Ideal Coordinates CCD File
C [auth A]~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,4-bis(oxidanyl)oxan-3-yl]ethanamide
C14 H25 N O11
KFEUJDWYNGMDBV-LODBTCKLSA-N
NI
(Subject of Investigation/LOI)

Query on NI



Download:Ideal Coordinates CCD File
D [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.154α = 90
b = 49.154β = 90
c = 160.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-11-12 
  • Deposition Author(s): Su, J.Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release