2VRP

Structure of rhodocytin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Rhodocytin, a Ligand for the Platelet-Activating Receptor Clec-2.

Watson, A.A.Eble, J.A.O'Callaghan, C.A.

(2008) Protein Sci 17: 1611

  • DOI: 10.1110/ps.035568.108
  • Primary Citation of Related Structures:  
    2VRP

  • PubMed Abstract: 
  • Binding of the snake venom protein rhodocytin to CLEC-2, a receptor on the surface of human platelets, initiates a signaling cascade leading to platelet activation and aggregation. We have previously solved the structure of CLEC-2. The 2.4 A resolution crystal structure of rhodocytin presented here demonstrates that it is the first snake venom or other C-type lectin-like protein to assemble as a non-disulfide linked (alphabeta)(2) tetramer ...

    Binding of the snake venom protein rhodocytin to CLEC-2, a receptor on the surface of human platelets, initiates a signaling cascade leading to platelet activation and aggregation. We have previously solved the structure of CLEC-2. The 2.4 A resolution crystal structure of rhodocytin presented here demonstrates that it is the first snake venom or other C-type lectin-like protein to assemble as a non-disulfide linked (alphabeta)(2) tetramer. Rhodocytin is highly adapted for interaction with CLEC-2 and displays a concave binding surface, which is highly complementary to the experimentally determined binding interface on CLEC-2. Using computational dynamic methods, surface electrostatic charge and hydrophobicity analyses, and protein-protein docking predictions, we propose that the (alphabeta)(2) rhodocytin tetramer induces clustering of CLEC-2 receptors on the platelet surface, which will trigger major signaling events resulting in platelet activation and aggregation.


    Organizational Affiliation

    Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AGGRETIN ALPHA CHAINA136Calloselasma rhodostomaMutation(s): 0 
UniProt
Find proteins for Q9I841 (Calloselasma rhodostoma)
Explore Q9I841 
Go to UniProtKB:  Q9I841
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AGGRETIN BETA CHAINB123Calloselasma 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: 2.41 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.933α = 90
b = 89.368β = 90
c = 120.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance