2LVZ

Solution structure of a Eosinophil Cationic Protein-trisaccharide heparin mimetic complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Insights into the glycosaminoglycan-mediated cytotoxic mechanism of eosinophil cationic protein revealed by NMR.

Garcia-Mayoral, M.F.Canales, A.Diaz, D.Lopez-Prados, J.Moussaoui, M.de Paz, J.L.Angulo, J.Nieto, P.M.Jimenez-Barbero, J.Boix, E.Bruix, M.

(2013) Acs Chem.Biol. 8: 144-151

  • DOI: 10.1021/cb300386v

  • PubMed Abstract: 
  • Protein-glycosaminoglycan interactions are essential in many biological processes and human diseases, yet how their recognition occurs is poorly understood. Eosinophil cationic protein (ECP) is a cytotoxic ribonuclease that interacts with glycosamino ...

    Protein-glycosaminoglycan interactions are essential in many biological processes and human diseases, yet how their recognition occurs is poorly understood. Eosinophil cationic protein (ECP) is a cytotoxic ribonuclease that interacts with glycosaminoglycans at the cell surface; this promotes the destabilization of the cellular membrane and triggers ECP's toxic activity. To understand this membrane destabilization event and the differences in the toxicity of ECP and its homologues, the high resolution solution structure of the complex between full length folded ECP and a heparin-derived trisaccharide (O-iPr-α-D-GlcNS6S-α(1-4)-L-IdoA2S-α(1-4)-D-GlcNS6S) has been solved by NMR methods and molecular dynamics simulations. The bound protein retains the tertiary structure of the free protein. The (2)S(0) conformation of the IdoA ring is preferably recognized by the protein. We have identified the precise location of the heparin binding site, dissected the specific interactions responsible for molecular recognition, and defined the structural requirements for this interaction. The structure reveals the contribution of Arg7, Gln14, and His15 in helix α1, Gln40 in strand β1, His64 in loop 4, and His128 in strand β6 in the recognition event and corroborates the previously reported participation of residues Arg34-Asn39. The participation of the catalytic triad (His15, Lys38, His128) in recognizing the heparin mimetic reveals, at atomic resolution, the mechanism of heparin's inhibition of ECP's ribonucleolytic activity. We have integrated all the available data to propose a molecular model for the membrane interaction process. The solved NMR complex provides the structural model necessary to design inhibitors to block ECP's toxicity implicated in eosinophil pathologies.


    Organizational Affiliation

    Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eosinophil cationic protein
A
133Homo sapiensMutation(s): 0 
Gene Names: RNASE3 (ECP, RNS3)
EC: 3.1.27.-
Find proteins for P12724 (Homo sapiens)
Go to Gene View: RNASE3
Go to UniProtKB:  P12724
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LVZ
Query on LVZ

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Download CCD File 
A
propan-2-yl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside
C9 H19 N O11 S2
OLCFKZNXXBRVTA-OKNNCHMLSA-N
 Ligand Interaction
SGN
Query on SGN

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Download CCD File 
A
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
IDS
Query on IDS

Download SDF File 
Download CCD File 
A
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release