6LSQ

Crystal structure of Echistatin, an RGD-containing short disintegrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural Insight into Integrin Recognition and Anticancer Activity of Echistatin.

Chen, Y.C.Chang, Y.T.Chen, C.Y.Shiu, J.H.Cheng, C.H.Huang, C.H.Chen, J.F.Chuang, W.J.

(2020) Toxins (Basel) 12

  • DOI: 10.3390/toxins12110709
  • Primary Citation of Related Structures:  
    6LSQ

  • PubMed Abstract: 
  • Echistatin (Ech) is a short disintegrin with a long 42 NPHKGPAT C-terminal tail. We determined the 3-D structure of Ech by X-ray crystallography. Superimposition of the structures of chains A and B showed conformational differences in their RGD loops and C-termini ...

    Echistatin (Ech) is a short disintegrin with a long 42 NPHKGPAT C-terminal tail. We determined the 3-D structure of Ech by X-ray crystallography. Superimposition of the structures of chains A and B showed conformational differences in their RGD loops and C-termini. The chain A structure is consistent with our NMR analysis that the GPAT residues of the C-terminus cannot be observed due to high flexibility. The hydrogen bond patterns of the RGD loop and between the RGD loop and C-terminus in Ech were the same as those of the corresponding residues in medium disintegrins. The mutant with C-terminal HKGPAT truncation caused 6.4-, 7.0-, 11.7-, and 18.6-fold decreases in inhibiting integrins αvβ3, αIIbβ3, αvβ5, and α5β1. Mutagenesis of the C-terminus showed that the H44A mutant caused 2.5- and 4.4-fold increases in inhibiting αIIbβ3 and α5β1, and the K45A mutant caused a 2.6-fold decrease in inhibiting αIIbβ3. We found that Ech inhibited VEGF-induced HUVEC proliferation with an IC 50 value of 103.2 nM and inhibited the migration of A375, U373MG, and Panc-1 tumor cells with IC 50 values of 1.5, 5.7, and 154.5 nM. These findings suggest that Ech is a potential anticancer agent, and its C-terminal region can be optimized to improve its anticancer activity.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, National Cheng Kung University College of Medicine, Tainan 70101, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DisintegrinA, B51Echis carinatusMutation(s): 0 
UniProt
Find proteins for E9JGG9 (Echis carinatus sochureki)
Explore E9JGG9 
Go to UniProtKB:  E9JGG9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.906α = 90
b = 33.906β = 90
c = 121.172γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
XDSphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release