3WWK

Crystal structure of CLEC-2 in complex with rhodocytin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 

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:  
    3WWK, 3WSR

  • 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 ...

    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. Electronic address: yyoshiki@riken.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-type lectin domain family 1 member BA [auth C], L [auth F], F [auth I], K [auth L]128Homo sapiensMutation(s): 1 
Gene Names: CLEC1B, CLEC2, UNQ721/PRO1384
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P126 (Homo sapiens)
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Go to UniProtKB:  Q9P126
PHAROS:  Q9P126
GTEx:  ENSG00000165682
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Snaclec rhodocytin subunit alphaB [auth A], D, G, I [auth J]136Calloselasma rhodostomaMutation(s): 0 
UniProt
Find proteins for Q9I841 (Calloselasma rhodostoma)
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Go to UniProtKB:  Q9I841
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Snaclec rhodocytin subunit betaC [auth B], E, H, J [auth K]146Calloselasma rhodostomaMutation(s): 0 
UniProt
Find proteins for Q9I840 (Calloselasma rhodostoma)
Explore Q9I840 
Go to UniProtKB:  Q9I840
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.851α = 90
b = 117.072β = 115.78
c = 152.238γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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