2JWM

NMR spatial srtucture of ternary complex kalata B7/Mn2+/DPC micelle


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Divalent cation coordination and mode of membrane interaction in cyclotides: NMR spatial structure of ternary complex Kalata B7/Mn(2+)/DPC micelle

Shenkarev, Z.O.Nadezhdin, K.D.Lyukmanova, E.N.Sobol, V.A.Skjeldal, L.Arseniev, A.S.

(2008) J.Inorg.Biochem. 102: 1246-1256

  • DOI: 10.1016/j.jinorgbio.2008.01.018

  • PubMed Abstract: 
  • The cyclotides are the family of hydrophobic bioactive plant peptides, characterized by a circular protein backbone and three knot forming disulfide bonds. It is believed that membrane activity of the cyclotides underlines their antimicrobial, cytoto ...

    The cyclotides are the family of hydrophobic bioactive plant peptides, characterized by a circular protein backbone and three knot forming disulfide bonds. It is believed that membrane activity of the cyclotides underlines their antimicrobial, cytotoxic and hemolytic properties, but the specific interactions with divalent cations can be also involved. To assess the mode of membrane interaction and divalent cation coordination in cyclotides, the spatial structure of the Möbius cyclotide Kalata B7 from the African perennial plant Oldenlandia affinis was determined in the presence of anisotropic membrane mimetic (dodecylphosphocholine micelles). The model of peptide/cation/micelle complex was built using 5-doxylstearate and Mn2+ relaxation probes. Results show that the peptide binds to the micelle surface with relatively high affinity by two hydrophobic loops (loop 2 - Thr6-Leu7 and loop 5 - Trp19-Ile21). The partially hydrated divalent cation is coordinated by charged side-chain of Glu3, aromatic side chain of Tyr11 and free carbonyls of Thr4 and Thr9, and is located in direct contact with the polar head-groups of detergent. The comparison with data about other cyclotides indicates that divalent cation coordination is the invariant property of all cyclotides, but the mode of peptide/membrane interactions is varied. Probably, the specific cation/peptide interactions play a major, but yet not known, role in the biological activity of the cyclotides.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kalata-B7
A
29Oldenlandia affinisMutation(s): 0 
Gene Names: OAK3
Find proteins for P58457 (Oldenlandia affinis)
Go to UniProtKB:  P58457
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • Olderado: 2JWM Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance