PDBsum entry 3wsr

Sugar binding protein

PDB id: 3wsr

Contents

Protein chains

120 a.a.

11 a.a.

Ligands

ALA-GLU-ASP-ASP-VAL-VAL-THR-PRO-GLY-CYS

A2G-GAL-SIA ×2

Waters ×36

PDB id:

3wsr

Name:

Sugar binding protein

Title:

Crystal structure of clec-2 in complex with o-glycosylated podoplanin

Structure:

C-type lectin domain family 1 member b. Chain: a, b. Fragment: clec-2, unp residues 96-221. Synonym: c-type lectin-like receptor 2, clec-2. Engineered: yes. Mutation: yes. Peptide from podoplanin. Chain: c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: clec1b, clec2, unq721/pro1384. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.91Å R-factor: 0.219 R-free: 0.259

Authors:

M.Nagae,K.Morita-Matsumoto,M.Kato,M.Kato-Kaneko,Y.Kato,Y.Yamaguchi

Key ref:

M.Nagae et al. (2014). A platform of C-type lectin-like receptor CLEC-2 for binding O-glycosylated podoplanin and nonglycosylated rhodocytin. Structure, 22, 1711-1721. PubMed id: 25458834 DOI: 10.1016/j.str.2014.09.009

Date:

20-Mar-14 Release date: 22-Oct-14

Protein chains

Q9P126  (CLC1B_HUMAN) -  C-type lectin domain family 1 member B from Homo sapiens

Seq: 229 a.a.

Struc: 120 a.a.

Protein chain

Q86YL7  (PDPN_HUMAN) -  Podoplanin from Homo sapiens

Seq: 162 a.a.

Struc: 11 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.str.2014.09.009

Structure 22:1711-1721 (2014)

PubMed id: 25458834

A platform of C-type lectin-like receptor CLEC-2 for binding O-glycosylated podoplanin and nonglycosylated rhodocytin.

M.Nagae, K.Morita-Matsumoto, M.Kato, M.K.Kaneko, Y.Kato, Y.Yamaguchi.

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.