3WWK

Crystal structure of CLEC-2 in complex with rhodocytin

Summary for 3WWK

• Entry DOI: 10.2210/pdb3wwk/pdb
• Related: 3WSR
• Descriptor: C-type lectin domain family 1 member B, Snaclec rhodocytin subunit alpha, Snaclec rhodocytin subunit beta (3 entities in total)
• Functional Keywords: c-type lectin fold, carbohydrate binding, podoplanin, rhodocytin, sugar binding protein
• Biological source: Homo sapiens (human); More
• Cellular location: Membrane ; Single-pass type II membrane protein : Q9P126; Secreted: Q9I841 Q9I840
• Total number of polymer chains: 12
• Total formula weight: 191038.08

Authors

Nagae, M.,Morita-Matsumoto, K.,Kato, M.,Kato-Kaneko, M.,Kato, Y.,Yamaguchi, Y. (deposition date: 2014-06-20, release date: 2014-10-22, Last modification date: 2024-10-09)

Primary citation

Nagae, M.,Morita-Matsumoto, K.,Kato, M.,Kato-Kaneko, M.,Kato, Y.,Yamaguchi, Y.
A Platform of C-type Lectin-like Receptor CLEC-2 for Binding O-Glycosylated Podoplanin and Nonglycosylated Rhodocytin
Structure, 22:1711-1721, 2014

PubMed Abstract: Podoplanin is a transmembrane O-glycoprotein that binds to C-type lectin-like receptor 2 (CLEC-2). The O-glycan-dependent interaction seems to play crucial roles in various biological processes, such as platelet aggregation. Rhodocytin, a snake venom, also binds to CLEC-2 and aggregates platelets in a glycan-independent manner. To elucidate the structural basis of the glycan-dependent and independent interactions, we performed comparative crystallographic studies of podoplanin and rhodocytin in complex with CLEC-2. Both podoplanin and rhodocytin bind to the noncanonical "side" face of CLEC-2. There is a common interaction mode between consecutive acidic residues on the ligands and the same arginine residues on CLEC-2. Other interactions are ligand-specific. Carboxyl groups from the sialic acid residue on podoplanin and from the C terminus of the rhodocytin α subunit interact differently at this "second" binding site on CLEC-2. The unique and versatile binding modes open a way to understand the functional consequences of CLEC-2-ligand interactions.

PubMed: 25458834
DOI: 10.1016/j.str.2014.09.009

Experimental method

X-RAY DIFFRACTION (2.98 Å)