5NQ4

Cytotoxin-1 in DPC-micelle


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin.

Dubovskii, P.V.Dubinnyi, M.A.Volynsky, P.E.Pustovalova, Y.E.Konshina, A.G.Utkin, Y.N.Arseniev, A.S.Efremov, R.G.

(2018) J. Biomol. Struct. Dyn. 36: 3463-3478

  • DOI: 10.1080/07391102.2017.1389662

  • PubMed Abstract: 
  • Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work, we investigated the interaction of CTs with phospholipid bilayers, u ...

    Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work, we investigated the interaction of CTs with phospholipid bilayers, using coarse-grained (CG) and full-atom (FA) molecular dynamics (MD). The object of this work is a CT of an S-type, cytotoxin I (CT1) from N.oxiana venom. Its spatial structure in aqueous solution and in the micelles of dodecylphosphocholine (DPC) were determined by 1H-NMR spectroscopy. Then, via CG- and FA MD-computations, we evaluated partitioning of CT1 molecule into palmitoyloleoylphosphatidylcholine (POPC) membrane, using the toxin spatial models, obtained either in aqueous solution, or detergent micelle. The latter model exhibits minimal structural changes upon partitioning into the membrane, while the former deviates from the starting conformation, loosing the tightly bound water molecule in the loop-2. These data show that the structural changes elicited by CT1 molecule upon incorporation into DPC micelle take place likely in the lipid membrane, although the mode of the interaction of this toxin with DPC micelle (with the tips of the all three loops) is different from its mode in POPC membrane (primarily with the tip of the loop-1 and both the tips of the loop-1 and loop-2).


    Related Citations: 
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytotoxin 1
A
60Naja oxianaMutation(s): 0 
Find proteins for P01451 (Naja oxiana)
Go to UniProtKB:  P01451
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 2.0: 2018-02-21
    Type: Atomic model
  • Version 2.1: 2019-01-16
    Type: Data collection, Database references