3WSR

Crystal structure of CLEC-2 in complex with O-glycosylated podoplanin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Platform of C-type Lectin-like Receptor CLEC-2 for Binding O-Glycosylated Podoplanin and Nonglycosylated Rhodocytin

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

(2014) Structure 22: 1711-1721

  • DOI: 10.1016/j.str.2014.09.009
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 1 member B
A, B
128Homo sapiensMutation(s): 1 
Gene Names: CLEC1B (CLEC2)
Find proteins for Q9P126 (Homo sapiens)
Go to Gene View: CLEC1B
Go to UniProtKB:  Q9P126
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from Podoplanin
C, D
18Homo sapiensMutation(s): 0 
Gene Names: PDPN (GP36)
Find proteins for Q86YL7 (Homo sapiens)
Go to Gene View: PDPN
Go to UniProtKB:  Q86YL7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
C, D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
C, D
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
C, D
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.369α = 90.00
b = 51.194β = 112.77
c = 54.099γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SERGUIdata collection
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description