1J2L

Crystal structure of the disintegrin, trimestatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Trimestatin, a Disintegrin Containing a Cell Adhesion Recognition Motif RGD

Fujii, Y.Okuda, D.Fujimoto, Z.Horii, T.Morita, T.Mizuno, H.

(2003) J.Mol.Biol. 332: 1115-1122


  • PubMed Abstract: 
  • Disintegrins are a family of small proteins containing an Arg-Gly-Asp (RGD) sequence motif that binds specifically to integrin receptors. Since the integrin is known to serve as the final common pathway leading to aggregation via formation of platele ...

    Disintegrins are a family of small proteins containing an Arg-Gly-Asp (RGD) sequence motif that binds specifically to integrin receptors. Since the integrin is known to serve as the final common pathway leading to aggregation via formation of platelet-platelet bridges, disintegrins act as fibrinogen receptor antagonists. Here, we report the first crystal structure of a disintegrin, trimestatin, found in snake venom. The structure of trimestatin at 1.7A resolution reveals that a number of turns and loops form a rigid core stabilized by six disulfide bonds. Electron densities of the RGD sequence are visible clearly at the tip of a hairpin loop, in such a manner that the Arg and Asp side-chains point in opposite directions. A docking model using the crystal structure of integrin alphaVbeta3 suggests that the Arg binds to the propeller domain, and Asp to the betaA domain. This model indicates that the C-terminal region is another potential binding site with integrin receptors. In addition to the RGD sequence, the structural evidence of a C-terminal region (Arg66, Trp67 and Asn68) important for disintegrin activity allows understanding of the high affinity and selectiveness of snake venom disintegrin for integrin receptors. The crystal structure of trimestatin should provide a useful framework for designing and developing more effective drugs for controlling platelet aggregation and anti-angiogenesis cancer.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies of dimeric disintegrins from the venom of two Agkistrodon snakes.
      Fujii, Y.,Okuda, D.,Fujimoto, Z.,Morita, T.,Mizuno, H.
      (2002) Acta Crystallogr.,Sect.D 58: 145
    • Purification and characterization of a new RGD/KGD-containing dimeric disintegrin, piscivostatin, from the venom of Agkistrodon piscivorus piscivorus: the unique effect of piscivostatin on platelet aggregation.
      Okuda, D.,Morita, T.
      (2001) J.Biochem.(Tokyo) 130: 407


    Organizational Affiliation

    Department of Biochemistry, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disintegrin triflavin
A
70Protobothrops flavoviridisN/A
Find proteins for P21859 (Protobothrops flavoviridis)
Go to UniProtKB:  P21859
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.546α = 90.00
b = 48.119β = 126.80
c = 37.667γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance