Eosinophil-derived Neurotoxin (EDN) - Adenosine 2'-5'-Diphosphate Complex

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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This is version 1.3 of the entry. See complete history


Mapping the Ribonucleolytic Active Site of Eosinophil-Derived Neurotoxin (Edn): High Resolution Crystal Structures of Edn Complexes with Adenylic Nucleotide Inhibitors

Leonidas, D.D.Boix, E.Prill, R.Suzuki, M.Turton, R.Minson, K.Swaminathan, G.J.Youle, R.J.Acharya, K.R.

(2001) J Biol Chem 276: 15009

  • DOI: https://doi.org/10.1074/jbc.M010585200
  • Primary Citation of Related Structures:  
    1HI2, 1HI3, 1HI4, 1HI5

  • PubMed Abstract: 

    Eosinophil-derived neurotoxin (EDN), a basic ribonuclease found in the large specific granules of eosinophils, belongs to the pancreatic RNase A family. Although its physiological function is still unclear, it has been shown that EDN is a neurotoxin capable of inducing the Gordon phenomenon in rabbits. EDN is also a potent helminthotoxin and can mediate antiviral activity of eosinophils against isolated virions of the respiratory syncytial virus. EDN is a catalytically efficient RNase sharing similar substrate specificity with pancreatic RNase A with its ribonucleolytic activity being absolutely essential for its neurotoxic, helminthotoxic, and antiviral activities. The crystal structure of recombinant human EDN in the unliganded form has been determined previously (Mosimann, S. C., Newton, D. L., Youle, R. J., and James, M. N. G. (1996) J. Mol. Biol. 260, 540-552). We have now determined high resolution (1.8 A) crystal structures for EDN in complex with adenosine-3',5'-diphosphate (3',5'-ADP), adenosine-2',5'-di-phosphate (2',5'-ADP), adenosine-5'-diphosphate (5'-ADP) as well as for a native structure in the presence of sulfate refined at 1.6 A. The inhibition constant of these mononucleotides for EDN has been determined. The structures present the first detailed picture of differences between EDN and RNase A in substrate recognition at the ribonucleolytic active site. They also provide a starting point for the design of tight-binding inhibitors, which may be used to restrain the RNase activity of EDN.

  • Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EOSINOPHIL-DERIVED NEUROTOXIN135Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10153 (Homo sapiens)
Explore P10153 
Go to UniProtKB:  P10153
PHAROS:  P10153
GTEx:  ENSG00000169385 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10153
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on A2P

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Binding Affinity Annotations 
IDSourceBinding Affinity
A2P Binding MOAD:  1HI3 Ki: 6.40e+4 (nM) from 1 assay(s)
PDBBind:  1HI3 Ki: 6.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.525α = 90
b = 56.176β = 90
c = 41.473γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-30
    Changes: Data collection, Structure summary