1GQV

Atomic Resolution (0.98A) Structure of Eosinophil-Derived Neurotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic Resolution (0.98 A) Structure of Eosinophil-Derived Neurotoxin

Swaminathan, G.J.Holloway, D.E.Veluraja, K.Acharya, K.R.

(2002) Biochemistry 41: 3341


  • PubMed Abstract: 
  • Human eosinophil-derived neurotoxin (EDN) is a small, basic protein that belongs to the ribonuclease A superfamily. EDN displays antiviral activity and causes the neurotoxic Gordon phenomenon when injected into rabbits. Although EDN and ribonuclease ...

    Human eosinophil-derived neurotoxin (EDN) is a small, basic protein that belongs to the ribonuclease A superfamily. EDN displays antiviral activity and causes the neurotoxic Gordon phenomenon when injected into rabbits. Although EDN and ribonuclease A have appreciable structural similarity and a conserved catalytic triad, their peripheral substrate-binding sites are not conserved. The crystal structure of recombinant EDN (rEDN) has been determined at 0.98 A resolution from data collected at a low temperature (100 K). We have refined the crystallographic model of the structure using anisotropic displacement parameters to a conventional R-factor of 0.116. This represents the highest resolution structure of rEDN determined to date and is only the second ribonuclease structure to be determined at a resolution greater than 1.0 A. The structure provides a detailed picture of the conformational freedom at the various subsites of rEDN, and the water structure accounts for more than 50% of the total solvent content of the unit cell. This information will be crucial for the design of tight-binding inhibitors to restrain the ribonucleolytic activity of rEDN.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EOSINOPHIL-DERIVED NEUROTOXIN
A
135Homo sapiensMutation(s): 0 
Gene Names: RNASE2 (EDN, RNS2)
EC: 3.1.27.5
Find proteins for P10153 (Homo sapiens)
Go to Gene View: RNASE2
Go to UniProtKB:  P10153
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.024α = 90.00
b = 57.477β = 90.00
c = 42.398γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SHELXL-97refinement
SCALEPACKdata scaling
AMoREphasing
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance