3VYK

Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 in complex with N-glycan

Summary for 3VYK

• Entry DOI: 10.2210/pdb3vyk/pdb
• Related: 3VYJ
• Descriptor: C-type lectin domain family 4, member a4, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: c-type lectin fold, cell surface, carbohydrate binding protein
• Biological source: Mus musculus (mouse)
• Total number of polymer chains: 1
• Total formula weight: 16382.95

Authors

Nagae, M.,Yamanaka, K.,Hanashima, S.,Ikeda, A.,Satoh, T.,Matsumoto, N.,Yamamoto, K.,Yamaguchi, Y. (deposition date: 2012-09-26, release date: 2013-10-02, Last modification date: 2024-11-20)

Primary citation

Nagae, M.,Yamanaka, K.,Hanashima, S.,Ikeda, A.,Morita-Matsumoto, K.,Satoh, T.,Matsumoto, N.,Yamamoto, K.,Yamaguchi, Y.
Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2
J.Biol.Chem., 288:33598-33610, 2013

PubMed Abstract: Dendritic cell inhibitory receptor 2 (DCIR2) is a C-type lectin expressed on classical dendritic cells. We recently identified the unique ligand specificity of mouse DCIR2 (mDCIR2) toward biantennary complex-type glycans containing bisecting N-acetylglucosamine (GlcNAc). Here, we report the crystal structures of the mDCIR2 carbohydrate recognition domain in unliganded form as well as in complex with an agalactosylated complex-type N-glycan unit carrying a bisecting GlcNAc residue. Bisecting GlcNAc and the α1-3 branch of the biantennary oligosaccharide asymmetrically interact with canonical and non-canonical mDCIR2 residues. Ligand-protein interactions occur directly through mDCIR2-characteristic amino acid residues as well as via a calcium ion and water molecule. Our structural and biochemical data elucidate for the first time the unique binding mode of mDCIR2 for bisecting GlcNAc-containing glycans, a mode that contrasts sharply with that of other immune C-type lectin receptors such as DC-SIGN.

PubMed: 24108122
DOI: 10.1074/jbc.M113.513572

Experimental method

X-RAY DIFFRACTION (1.5 Å)