5B1W

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

Summary for 5B1W

• Entry DOI: 10.2210/pdb5b1w/pdb
• Related: 5B1X
• Descriptor: C-type lectin domain family 4 member A, CALCIUM ION (3 entities in total)
• Functional Keywords: c-type lectin domain, innate immunity, carbohydrate recognition, carbohydrate binding protein
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 63570.54

Authors

Nagae, M.,Yamaguchi, Y. (deposition date: 2015-12-21, release date: 2016-05-11, Last modification date: 2023-11-08)

Primary citation

Nagae, M.,Ikeda, A.,Hanashima, S.,Kojima, T.,Matsumoto, N.,Yamamoto, K.,Yamaguchi, Y.
Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan
Febs Lett., 590:1280-1288, 2016

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 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 (GlcNAcβ1-2Man) 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.

PubMed: 27015765
DOI: 10.1002/1873-3468.12162

Experimental method

X-RAY DIFFRACTION (3.05 Å)