Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.34 kDa 
• Atom Count: 226 
• Modelled Residue Count: 31 
• Deposited Residue Count: 31 
• Unique protein chains: 1

1ZA8

NMR solution structure of a leaf-specific-expressed cyclotide vhl-1

• PDB DOI: 10.2210/pdb1ZA8/pdb
• BMRB: 6596

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Viola hederacea
• Mutation(s): No 


• Deposited: 2005-04-05 Released: 2005-04-12 
• Deposition Author(s): Chen, B., Colgrave, M.L., Daly, N.L., Rosengren, K.J., Gustafson, K.R., Craik, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Isolation and characterization of novel cyclotides from Viola hederaceae: solution structure and anti-HIV activity of vhl-1, a leaf-specific expressed cyclotide.

Chen, B., Colgrave, M.L., Daly, N.L., Rosengren, K.J., Gustafson, K.R., Craik, D.J.

(2005) J Biol Chem 280: 22395-22405

• PubMed: 15824119 
• DOI: 10.1074/jbc.M501737200
• Primary Citation of Related Structures:  
  1ZA8


• PubMed Abstract: 
  

Based on a newly established sequencing strategy featured by its efficiency, simplicity, and easy manipulation, the sequences of four novel cyclotides (macrocyclic knotted proteins) isolated from an Australian plant Viola hederaceae were determined. The three-dimensional solution structure of V. hederaceae leaf cyclotide-1 (vhl-1), a leaf-specific expressed 31-residue cyclotide, has been determined using two-dimensional (1)H NMR spectroscopy. vhl-1 adopts a compact and well defined structure including a distorted triple-stranded beta-sheet, a short 3(10) helical segment and several turns. It is stabilized by three disulfide bonds, which, together with backbone segments, form a cyclic cystine knot motif. The three-disulfide bonds are almost completely buried into the protein core, and the six cysteines contribute only 3.8% to the molecular surface. A pH titration experiment revealed that the folding of vhl-1 shows little pH dependence and allowed the pK(a) of 3.0 for Glu(3) and approximately 5.0 for Glu(14) to be determined. Met(7) was found to be oxidized in the native form, consistent with the fact that its side chain protrudes into the solvent, occupying 7.5% of the molecular surface. vhl-1 shows anti-HIV activity with an EC(50) value of 0.87 microm.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vhl-1	A	31	Viola hederacea	Mutation(s): 0
UniProt
Find proteins for P84522 (Viola hederacea) Explore P84522  Go to UniProtKB:  P84522

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 1ZA8 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-05 
• Released Date: 2005-04-12 
Deposition Author(s): Chen, B., Colgrave, M.L., Daly, N.L., Rosengren, K.J., Gustafson, K.R., Craik, D.J.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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