Crystal structure of human galectin-9 C-terminal CRD

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose

Yoshida, H.Teraoka, M.Nishi, N.Nakakita, S.Nakamura, T.Hirashima, M.Kamitori, S.

(2010) J Biol Chem 285: 36969-36976

  • DOI: https://doi.org/10.1074/jbc.M110.163402
  • Primary Citation of Related Structures:  
    3NV1, 3NV2, 3NV3, 3NV4

  • PubMed Abstract: 

    Galectin-9, a tandem-repeat-type β-galactoside-specific animal lectin with two carbohydrate recognition domains (CRDs) at the N- and C-terminal ends, is involved in chemoattraction, apoptosis, and the regulation of cell differentiation and has anti-allergic effects. Its ability to recognize carbohydrates is essential for its biological functions. Human galectin-9 (hG9) has high affinity for branched N-glycan-type oligosaccharides (dissociation constants of 0.16-0.70 μM) and linear β1-3-linked poly-N-acetyllactosamines (0.09-8.3 μM) and significant affinity for the α2-3-sialylated oligosaccharides (17-34 μM). Further, its N-terminal CRD (hG9N) and C-terminal CRD (hG9C) differ in specificity. To elucidate this unique feature of hG9, x-ray structures of hG9C in the free form and in complexes with N-acetyllactosamine, the biantennary pyridylaminated oligosaccharide, and α2-3-sialyllactose were determined. They are the first x-ray structural analysis of C-terminal CRD of the tandem-repeat-type galectin. The results clearly revealed the mechanism by which branched and α2-3-sialylated oligosaccharides are recognized and explained the difference in specificity between hG9N and hG9C. Based on structural comparisons with other galectins, we propose that the wide entrance for ligand binding and the shallow binding site of hG9C are favorable for branched oligosaccharides and that Arg(221) is responsible for recognizing sialylated oligosaccharides.

  • Organizational Affiliation

    Life Science Research Center, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin 9 short isoform variant138Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O00182 (Homo sapiens)
Explore O00182 
Go to UniProtKB:  O00182
PHAROS:  O00182
GTEx:  ENSG00000168961 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00182
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NI

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.585α = 90
b = 70.585β = 90
c = 50.136γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description