X-ray crystal structure of ECP (RNase 3) at 1.75 A

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

Starting Model: other
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Three-Dimensional Crystal Structure of Human Eosinophil Cationic Protein (Rnase 3) at 1.75 A Resolution.

Mallorqui-Fernandez, G.Pous, J.Peracaula, R.Maeda, T.Tada, H.Yamada, H.Seno, M.De Llorens, R.Gomis-Rueth, F.X.Coll, M.

(2000) J Mol Biol 300: 1297

  • DOI: https://doi.org/10.1006/jmbi.2000.3939
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Eosinophil cationic protein (ECP; RNase 3) is a human ribonuclease found only in eosinophil leukocytes that belongs to the RNase A superfamily. This enzyme is bactericidal, helminthotoxic and cytotoxic to mammalian cells and tissues. The protein has been cloned, heterologously overexpressed, purified and crystallized. Its crystal structure has been determined and refined using data up to 1. 75 A resolution. The molecule displays the alpha+beta folding topology typical for members of the ribonuclease A superfamily. The catalytic active site residues are conserved with respect to other ribonucleases of the superfamily but some differences appear at substrate recognition subsites, which may account, in part, for the low catalytic activity. Most strikingly, 19 surface-located arginine residues confer a strong basic character to the protein. The high concentration of positive charges and the particular orientation of the side-chains of these residues may also be related to the low activity of ECP as a ribonuclease and provides an explanation for its unique cytotoxic role through cell membrane disruption.

  • Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, C.I.D-C.S.I.C, Jordi Girona, 18-26, Barcelona, 08034, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
133Homo sapiensMutation(s): 0 
Gene Names: RNASE3
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P12724 (Homo sapiens)
Explore P12724 
Go to UniProtKB:  P12724
GTEx:  ENSG00000169397 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12724
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.163α = 90
b = 62.163β = 90
c = 174.59γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-08
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2024-05-01
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description