3NV1

Crystal structure of human galectin-9 C-terminal CRD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1074/jbc.M110.163402
  • Primary Citation of Related Structures:  3NV2, 3NV3, 3NV4
  • Also Cited By: 4HL0

  • 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-a ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galectin 9 short isoform variant
A
138Homo sapiensGene Names: LGALS9
Find proteins for O00182 (Homo sapiens)
Go to Gene View: LGALS9
Go to UniProtKB:  O00182
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 70.585α = 90.00
b = 70.585β = 90.00
c = 50.136γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
MOLREPphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance