Crystal structure of the cyclotide varv F

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.224 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold

Wang, C.K.Hu, S.H.Martin, J.L.Hajdu, J.Bohlin, L.Claeson, P.Rosengren, K.J.Tang, J.Tan, N.H.Craik, D.J.

(2009) J Biol Chem 284: 10672-10683

  • DOI: https://doi.org/10.1074/jbc.M900021200
  • Primary Citation of Related Structures:  
    2K7G, 3E4H

  • PubMed Abstract: 

    Cyclotides are a family of plant defense proteins that are highly resistant to adverse chemical, thermal, and enzymatic treatment. Here, we present the first crystal structure of a cyclotide, varv F, from the European field pansy, Viola arvensis, determined at a resolution of 1.8 A. The solution state NMR structure was also determined and, combined with measurements of biophysical parameters for several cyclotides, provided an insight into the structural features that account for the remarkable stability of the cyclotide family. The x-ray data confirm the cystine knot topology and the circular backbone, and delineate a conserved network of hydrogen bonds that contribute to the stability of the cyclotide fold. The structural role of a highly conserved Glu residue that has been shown to regulate cyclotide function was also determined, verifying its involvement in a stabilizing hydrogen bond network. We also demonstrate that varv F binds to dodecylphosphocholine micelles, defining the binding orientation and showing that its structure remains unchanged upon binding, further demonstrating that the cyclotide fold is rigid. This study provides a biological insight into the mechanism by which cyclotides maintain their native activity in the unfavorable environment of predator insect guts. It also provides a structural basis for explaining how a cluster of residues important for bioactivity may be involved in self-association interactions in membranes. As well as being important for their bioactivity, the structural rigidity of cyclotides makes them very suitable as a stable template for peptide-based drug design.

  • Organizational Affiliation

    University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Varv peptide F,Varv peptide F29Viola arvensisMutation(s): 0 
Find proteins for P58451 (Viola arvensis)
Explore P58451 
Go to UniProtKB:  P58451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58451
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.224 
  • Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.081α = 90
b = 84.081β = 90
c = 84.081γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2009-02-10 
  • Deposition Author(s): Hu, S.H.

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description