8HB5 | pdb_00008hb5

Crystal structure of Mincle in complex with HD-275


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.336 (Depositor), 0.335 (DCC) 
  • R-Value Work: 
    0.296 (Depositor), 0.296 (DCC) 
  • R-Value Observed: 
    0.298 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

PGL-III, a Rare Intermediate of Mycobacterium leprae Phenolic Glycolipid Biosynthesis, Is a Potent Mincle Ligand.

Ishizuka, S.van Dijk, J.H.M.Kawakita, T.Miyamoto, Y.Maeda, Y.Goto, M.Le Calvez, G.Groot, L.M.Witte, M.D.Minnaard, A.J.van der Marel, G.A.Ato, M.Nagae, M.Codee, J.D.C.Yamasaki, S.

(2023) ACS Cent Sci 9: 1388-1399

  • DOI: https://doi.org/10.1021/acscentsci.3c00040
  • Primary Citation Related Structures: 
    8H4V, 8HB5

  • PubMed Abstract: 

    Although leprosy (Hansen's disease) is one of the oldest known diseases, the pathogenicity of Mycobacterium leprae ( M. leprae ) remains enigmatic. Indeed, the cell wall components responsible for the immune response against M. leprae are as yet largely unidentified. We reveal here phenolic glycolipid-III (PGL-III) as an M. leprae -specific ligand for the immune receptor Mincle. PGL-III is a scarcely present trisaccharide intermediate in the biosynthetic pathway to PGL-I, an abundant and characteristic M. leprae glycolipid. Using activity-based purification, we identified PGL-III as a Mincle ligand that is more potent than the well-known M. tuberculosis trehalose dimycolate. The cocrystal structure of Mincle and a synthetic PGL-III analogue revealed a unique recognition mode, implying that it can engage multiple Mincle molecules. In Mincle-deficient mice infected with M. leprae , increased bacterial burden with gross pathologies were observed. These results show that PGL-III is a noncanonical ligand recognized by Mincle, triggering protective immunity.


  • Organizational Affiliation
    • Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content 

  • Total Structure Weight: 17.76 kDa 
  • Atom Count: 1,213 
  • Modeled Residue Count: 146 
  • Deposited Residue Count: 151 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member E151Bos taurusMutation(s): 1 
Gene Names: CLEC4E
UniProt
Find proteins for E1BHM0 (Bos taurus)
Explore E1BHM0 
Go to UniProtKB:  E1BHM0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1BHM0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.336 (Depositor), 0.335 (DCC) 
  • R-Value Work:  0.296 (Depositor), 0.296 (DCC) 
  • R-Value Observed: 0.298 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.515α = 90
b = 97.515β = 90
c = 46.49γ = 120
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)Japan20H00505
Japan Society for the Promotion of Science (JSPS)Japan20K06575

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2026-03-04
    Changes: Refinement description