4ZES

Blood dendritic cell antigen 2 (BDCA-2) complexed with methyl-mannoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2.

Jegouzo, S.A.Feinberg, H.Dungarwalla, T.Drickamer, K.Weis, W.I.Taylor, M.E.

(2015) J.Biol.Chem. 290: 16759-16771

  • DOI: 10.1074/jbc.M115.660613
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Blood dendritic cell antigen 2 (BDCA-2; also designated CLEC4C or CD303) is uniquely expressed on plasmacytoid dendritic cells. Stimulation of BDCA-2 with antibodies leads to an anti-inflammatory response in these cells, but the natural ligands for t ...

    Blood dendritic cell antigen 2 (BDCA-2; also designated CLEC4C or CD303) is uniquely expressed on plasmacytoid dendritic cells. Stimulation of BDCA-2 with antibodies leads to an anti-inflammatory response in these cells, but the natural ligands for the receptor are not known. The C-type carbohydrate recognition domain in the extracellular portion of BDCA-2 contains a signature motif typical of C-type animal lectins that bind mannose, glucose, or GlcNAc, yet it has been reported that BDCA-2 binds selectively to galactose-terminated, biantennary N-linked glycans. A combination of glycan array analysis and binding competition studies with monosaccharides and natural and synthetic oligosaccharides have been used to define the binding epitope for BDCA-2 as the trisaccharide Gal╬▓1-3/4GlcNAc╬▓1-2Man. X-ray crystallography and mutagenesis studies show that mannose is ligated to the conserved Ca(2+) in the primary binding site that is characteristic of C-type carbohydrate recognition domains, and the GlcNAc and galactose residues make additional interactions in a wide, shallow groove adjacent to the primary binding site. As predicted from these studies, BDCA-2 binds to IgG, which bears galactose-terminated glycans that are not commonly found attached to other serum glycoproteins. Thus, BDCA-2 has the potential to serve as a previously unrecognized immunoglobulin Fc receptor.


    Organizational Affiliation

    the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 4 member C
A, B
147Homo sapiensMutation(s): 1 
Gene Names: CLEC4C (BDCA2, CLECSF11, CLECSF7, DLEC, HECL)
Find proteins for Q8WTT0 (Homo sapiens)
Go to Gene View: CLEC4C
Go to UniProtKB:  Q8WTT0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MMA
Query on MMA

Download SDF File 
Download CCD File 
A, B
O1-METHYL-MANNOSE
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.713α = 90.00
b = 69.576β = 90.00
c = 117.506γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom093599
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103393
National Institutes of Health/National Center for Research ResourcesUnited StatesP41RR001209
Department of Energy (United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2015-07-15
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence