9KPL | pdb_00009kpl

Crystal structure of T. rubripes Mincle with glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.180 (Depositor) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates.

Ito, T.Guenther, C.Ishikawa, E.Yabuki, T.Nagae, M.Nakatani, Y.Yamasaki, S.

(2025) Immunogenetics 77: 18-18

  • DOI: https://doi.org/10.1007/s00251-025-01375-x
  • Primary Citation Related Structures: 
    9KPL, 9KS7

  • PubMed Abstract: 

    Our bodies are continuously exposed to injurious insults by infection and tissue damage, which are primarily sensed by innate immune receptors to maintain homeostasis. Among such receptors is macrophage-inducible C-type lectin (Mincle, gene symbol CLEC4E), a member of the C-type lectin receptor (CLR) family, which functions as an immune sensor for both pathogens and damaged self. To monitor these injurious stimuli, Mincle recognizes disaccharide-based pathogen-derived glycolipids and monosaccharide-based intracellular metabolites, such as β-glucosylceramide. Mincle is well-conserved among mammals; however, there are questions that remain unclear, such as from which lower vertebrate did it arise and whether the original ligand was self or non-self. Here, we found homologues of Mincle and its signaling subunit Fc receptor γ chain (FcRγ) in lower vertebrates, such as reptiles, amphibians, and fishes. The crystal structure of a Mincle homologue revealed that fish Mincle possesses a narrower sugar-binding pocket than that of mammalian Mincle, and accommodates only monosaccharide moieties. These results suggest that Mincle may have evolved from a self-recognizing receptor, and its sugar-binding pocket widened during evolution, presumably to adapt to disaccharide-based glycolipids derived from life-threatening pathogens.


  • Organizational Affiliation
    • Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.

Macromolecule Content 

  • Total Structure Weight: 35.71 kDa 
  • Atom Count: 2,559 
  • Modeled Residue Count: 268 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain-containing proteinA,
B [auth E]
144Takifugu rubripesMutation(s): 0 
UniProt
Find proteins for A0A3B5KEF3 (Takifugu rubripes)
Explore A0A3B5KEF3 
Go to UniProtKB:  A0A3B5KEF3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B5KEF3
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on GLC



Download:Ideal Coordinates CCD File
C [auth A],
G [auth E]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
BGC
(Subject of Investigation/LOI)

Query on BGC



Download:Ideal Coordinates CCD File
D [auth A],
H [auth E]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth E],
J [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.180 (Depositor) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.353α = 90
b = 69.86β = 115.774
c = 51.584γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release