6LKR

Crystal structure of mouse DCAR2 CRD domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR.

Omahdi, Z.Horikawa, Y.Nagae, M.Toyonaga, K.Imamura, A.Takato, K.Teramoto, T.Ishida, H.Kakuta, Y.Yamasaki, S.

(2020) J.Biol.Chem. --: --

  • DOI: 10.1074/jbc.RA120.012491
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The C-type lectin receptors (CLRs) form a family of pattern recognition receptors (PRRs) that recognize numerous pathogens, such as bacteria and fungi, and trigger innate immune responses. The extracellular carbohydrate recognition domain (CRD) of CL ...

    The C-type lectin receptors (CLRs) form a family of pattern recognition receptors (PRRs) that recognize numerous pathogens, such as bacteria and fungi, and trigger innate immune responses. The extracellular carbohydrate recognition domain (CRD) of CLRs forms a globular structure that can coordinate a Ca 2+ ion, allowing receptor interactions with sugar-containing ligands. Although well conserved, the CRD fold can also display differences that directly affect the specificity of the receptors for their ligands. Here, we report crystal structures at 1.8-2.3 Å resolutions of the CRD of murine d endritic c ell-immuno a ctivating r eceptor (DCAR/ Clec4b1 ), the only CLR that binds phosphoglycolipids such as acylated phosphatidyl-myo-inositol mannosides (AcPIMs) of mycobacteria. Using mutagenesis analysis, we identified critical residues, Ala136 and Gln198, on the surface surrounding the ligand-binding site of DCAR, as well as an atypical Ca 2+ -binding motif (Glu-Pro-Ser/EPS 168-170 ). By chemically synthesizing a water-soluble ligand analog, inositol-monophosphate di-mannose (IPM2), we confirmed the direct interaction of DCAR with the polar moiety of AcPIMs by biolayer interferometry and co-crystallization approaches. We also observed a hydrophobic groove extending from the ligand-binding site that is in a suitable position to interact with the lipid portion of whole AcPIMs. These results suggest that the hydroxyl group-binding ability and hydrophobic groove of DCAR mediate its specific binding to pathogen-derived phosphoglycolipids such as mycobacterial AcPIMs.


    Organizational Affiliation

    Research Institute for Microbial Diseases, Osaka University, Japan.,Department of Pharmaceutical Sciences, The University of Tokyo, Japan.,Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Japan.,Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, Japan.,Gifu University.,Department of Applied Bioorganic Chemistry, Faculty of Applied Biological Sciences, Gifu University, Japan.,Kyushu University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 4, member b1
A, B
136Mus musculusMutation(s): 0 
Gene Names: Clec4b1 (Clec4b, Dcar)
Find proteins for Q9D8Q7 (Mus musculus)
Go to UniProtKB:  Q9D8Q7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download SDF File 
Download CCD File 
A
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.423α = 90.00
b = 72.068β = 90.00
c = 100.580γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
MOLREPphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release