6L6D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.233 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGA (Subject of Investigation/LOI)
Query on NGA

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.9α = 90
b = 48.9β = 90
c = 261.66γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NGAClick on this verticalbar to view details

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 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary