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 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 295: 5807-5817

  • DOI: 10.1074/jbc.RA120.012491
  • Structures With Same Primary Citation

  • 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.



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: Clec4b1Clec4bDcar
Find proteins for Q9D8Q7 (Mus musculus)
Go to UniProtKB:  Q9D8Q7
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

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 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 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.423α = 90
b = 72.068β = 90
c = 100.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references