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.,From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and.,the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom maureen.taylor@imperial.ac.uk.




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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMAKi: 9400000 nM BINDINGMOAD
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