6L6C

X-ray structure of human galectin-10 in complex with D-arabinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals.

Itoh, A.Nonaka, Y.Nakakita, S.I.Yoshida, H.Nishi, N.Nakamura, T.Kamitori, S.

(2020) Biochem Biophys Res Commun 

  • DOI: https://doi.org/10.1016/j.bbrc.2020.02.037
  • Primary Citation of Related Structures:  
    6L64, 6L67, 6L68, 6L6A, 6L6B, 6L6C, 6L6D

  • PubMed Abstract: 

    The galectins are a family of β-galactoside-specific animal lectins, and have attracted much attention as novel regulators of the immune system. Galectin-10 is well-expressed in eosinophils, and spontaneously forms Charcot-Leyden crystals (CLCs), during prolonged eosinophilic inflammatory reactions, which are frequently observed in eosinophilic diseases. Although biochemical and structural characterizations of galectin-10 have been done, its biological role and molecular mechanism are still unclear, and few X-ray structures of galectin-10 in complex with monosaccharides/oligosaccharides have been reported. Here, X-ray structures of galectin-10 in complexes with seven monosaccharides are presented with biochemical analyses to detect interactions of galectin-10 with monosaccharides/oligosaccharides. Galectin-10 forms a homo-dimer in the face-to-face orientation, and the monosaccharides bind to the carbohydrate recognition site composed of amino acid residues from two galectin-10 molecules of dimers, suggesting that galectin-10 dimer likely captures the monosaccharides in solution and in vivo. d-Glucose, d-allose, d-arabinose, and D-N-acetylgalactosamine bind to the interfaces between galectin-10 dimers in crystals, and they affect the stability of molecular packing in crystals, leading to easy-dissolving of CLCs, and/or inhibiting the formation of CLCs. These monosaccharides may serve as effectors of G10 to form CLCs in vivo.


  • Organizational Affiliation

    Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-10144Homo sapiensMutation(s): 1 
Gene Names: CLCLGALS10LGALS10A
UniProt & NIH Common Fund Data Resources
Find proteins for Q05315 (Homo sapiens)
Explore Q05315 
Go to UniProtKB:  Q05315
PHAROS:  Q05315
GTEx:  ENSG00000105205 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05315
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.78α = 90
b = 48.78β = 90
c = 260.21γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2020-03-04 
  • Deposition Author(s): Kamitori, S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary