5B1W

Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan

Nagae, M.Ikeda, A.Hanashima, S.Kojima, T.Matsumoto, N.Yamamoto, K.Yamaguchi, Y.

(2016) Febs Lett. 590: 1280-1288

  • DOI: 10.1002/1873-3468.12162
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human dendritic cell inhibitory receptor (DCIR) is a C-type lectin receptor expressed in classical dendritic cells and accepts several oligosaccharide ligands including N-glycans. Here, we report the crystal structures of human DCIR C-type lectin dom ...

    Human dendritic cell inhibitory receptor (DCIR) is a C-type lectin receptor expressed in classical dendritic cells and accepts several oligosaccharide ligands including N-glycans. Here, we report the crystal structures of human DCIR C-type lectin domains in the absence and presence of a branched N-glycan unit. The domain has a typical C-type lectin fold and two bound calcium ions. In the ligand-bound form, the disaccharide unit (GlcNAc╬▓1-2Man) acceptably fits the electron density map, indicating that it forms the main epitope. The recognition of the nonterminal N-glycan unit explains the relatively broad specificity of this lectin.


    Organizational Affiliation

    Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan.,Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 4 member A
A, B, C, D
134Homo sapiensMutation(s): 0 
Gene Names: CLEC4A (CLECSF6, DCIR, LLIR)
Find proteins for Q9UMR7 (Homo sapiens)
Go to Gene View: CLEC4A
Go to UniProtKB:  Q9UMR7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.489α = 90.00
b = 105.832β = 90.00
c = 65.387γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan24770111
MEXTJapan15K18496

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release