Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.83 kDa 
• Atom Count: 2909 
• Modelled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 1

4ZES

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

• PDB DOI: 10.2210/pdb4ZES/pdb

• Classification: Carbohydrate-binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-20 Released: 2015-05-27 
• Deposition Author(s): Jegouzo, S.A.F., Feinberg, H., Dungarwalla, T., Drickamer, K., Weis, W.I., Taylor, M.E.
• Funding Organization(s): Wellcome Trust, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.214 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

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

• PubMed: 25995448 
• DOI: 10.1074/jbc.M115.660613
• Primary Citation of Related Structures:  
  4ZES, 4ZET


• 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 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 Galβ1-3/4GlcNAcβ1-2Man. 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.

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Organizational Affiliation: 

the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 4 member C	A, B	147	Homo sapiens	Mutation(s): 1  Gene Names: CLEC4C, BDCA2, CLECSF11, CLECSF7, DLEC, HECL, UNQ9361/PRO34150
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTT0 (Homo sapiens) Explore Q8WTT0  Go to UniProtKB:  Q8WTT0
PHAROS:  Q8WTT0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMA	C [auth A], E [auth B]	methyl alpha-D-mannopyranoside C7 H14 O6 HOVAGTYPODGVJG-VEIUFWFVSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MMA	Binding MOAD:  4ZES	Ki: 9.40e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.214 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.713	α = 90
b = 69.576	β = 90
c = 117.506	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-20 
• Released Date: 2015-05-27 
Deposition Author(s): Jegouzo, S.A.F., Feinberg, H., Dungarwalla, T., Drickamer, K., Weis, W.I., Taylor, M.E.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	093599
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	P41RR001209
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2015-06-03
  Changes: Database references
• Version 1.2: 2015-07-15
  Changes: Database references
• Version 1.3: 2017-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence
• Version 1.5: 2019-12-04
  Changes: Author supporting evidence
• Version 1.6: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary