Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46502.06 
• Atom Count: 2844 
• Residue Count: 407 
• Unique protein chains: 1

4LEJ

Crystal Structure of the Korean pine (Pinus koraiensis) vicilin

• DOI: 10.2210/pdb4LEJ/pdb

• Classification: allergen plant protein
• Organism(s): Pinus koraiensis


• Deposited: 2013-06-25 Released: 2014-01-22 
• Deposition Author(s): Jin, T.C., Wang, Y., Zhang, Y.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.402 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 

Literature

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

• PubMed: 24328105 
• DOI: 10.1021/jf4039887


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vicilin	A	407	Pinus koraiensis	Mutation(s): 0
Find proteins for W5IDC2 (Pinus koraiensis) Go to UniProtKB:  W5IDC2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.402 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• Space Group: I 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 148.780	α = 90.00
b = 148.780	β = 90.00
c = 148.780	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
HKL-2000	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-25 
• Released Date: 2014-01-22 
• Deposition Author(s): Jin, T.C., Wang, Y., Zhang, Y.Z.

Revision History 

• Version 1.0: 2014-01-22
  Type: Initial release
• Version 1.1: 2014-10-15
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description