Crystal Structure of the Korean pine (Pinus koraiensis) vicilin

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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This is version 1.3 of the entry. See complete history


Crystal Structure of Korean Pine ( Pinus koraiensis ) 7S Seed Storage Protein with Copper Ligands.

Jin, T.Wang, Y.Chen, Y.W.Fu, T.J.Kothary, M.H.McHugh, T.H.Zhang, Y.

(2014) J Agric Food Chem 62: 222-228

  • DOI: https://doi.org/10.1021/jf4039887
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The prevalence of food allergy has increased in recent years, and Korean pine vicilin is a potential food allergen. We have previously reported the crystallization of Korean pine vicilin purified from raw pine nut. Here we report the isolation of vicilin mRNA and the crystal structure of Korean pine vicilin at 2.40 Å resolution. The overall structure of pine nut vicilin is similar to the structures of other 7S seed storage proteins and consists of an N-terminal domain and a C-terminal domain. Each assumes a cupin fold, and they are symmetrically related about a pseudodyad axis. Three vicilin molecules form a doughnut-shaped trimer through head-to-tail association. Structure characterization of Korean pine nut vicilin unexpectedly showed that, in its native trimeric state, the vicilin has three copper ligands. Sequence alignments suggested that the copper-coordinating residues were conserved in winter squash, sesame, tomato, and several tree nuts, while they were not conserved in a number of legumes, including peanut and soybean. Additional studies are needed to assess whether the copper-coordinating property of vicilins has a biological function in the relevant plants. The nutritional value of this copper-coordinating protein in tree nuts and other edible seeds may be worth further investigations.

  • Organizational Affiliation

    Department of Biology, Illinois Institute of Technology , 3101 South Dearborn Street, Chicago, Illinois 60616, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vicilin407Pinus koraiensisMutation(s): 0 
Find proteins for V9VGU0 (Pinus koraiensis)
Explore V9VGU0 
Go to UniProtKB:  V9VGU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9VGU0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.78α = 90
b = 148.78β = 90
c = 148.78γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations