1RL5

NMR structure with tightly bound water molecule of cytotoxin I from Naja oxiana in aqueous solution (major form)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins.

Dubovskii, P.V.Lesovoy, D.M.Dubinnyi, M.A.Konshina, A.G.Utkin, Y.N.Efremov, R.G.Arseniev, A.S.

(2005) Biochem J 387: 807-815

  • DOI: https://doi.org/10.1042/BJ20041814
  • Primary Citation of Related Structures:  
    1RL5, 1ZAD

  • PubMed Abstract: 

    The CTs (cytotoxins) I and II are positively charged three-finger folded proteins from venom of Naja oxiana (the Central Asian cobra). They belong to S- and P-type respectively based on Ser-28 and Pro-30 residues within a putative phospholipid bilayer binding site. Previously, we investigated the interaction of CTII with multilamellar liposomes of dipalmitoylphosphatidylglycerol by wide-line (31)P-NMR spectroscopy. To compare interactions of these proteins with phospholipids, we investigated the interaction of CTI with the multilamellar liposomes of dipalmitoylphosphatidylglycerol analogously. The effect of CTI on the chemical shielding anisotropy and deformation of the liposomes in the magnetic field was determined at different temperatures and lipid/protein ratios. It was found that both the proteins do not affect lipid organization in the gel state. In the liquid crystalline state of the bilayer they disturb lipid packing. To get insight into the interactions of the toxins with membranes, Monte Carlo simulations of CTI and CTII in the presence of the bilayer membrane were performed. It was found that both the toxins penetrate into the bilayer with the tips of all the three loops. However, the free-energy gain on membrane insertion of CTI is smaller (by approximately 7 kcal/mol; 1 kcal identical with 4.184 kJ) when compared with CTII, because of the lower hydrophobicity of the membrane-binding site of CTI. These results clearly demonstrate that the P-type cytotoxins interact with membranes stronger than those of the S-type, although the mode of the membrane insertion is similar for both the types.


  • Organizational Affiliation

    Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., V-437, Moscow 117997, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytotoxin 160Naja oxianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P01451 (Naja oxiana)
Explore P01451 
Go to UniProtKB:  P01451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01451
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations