Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 366.08 kDa 
• Atom Count: 19957 
• Residue Count: 3186 
• Unique protein chains: 1

3FZ3

Crystal Structure of almond Pru1 protein

• DOI: 10.2210/pdb3FZ3/pdb

• Classification: ALLERGEN
• Organism(s): Prunus dulcis
• Mutation(s): No 


• Deposited: 2009-01-23 Released: 2009-11-10 
• Deposition Author(s): Jin, T.C., Zhang, Y.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.229 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Crystal structure of prunin-1, a major component of the almond (Prunus dulcis) allergen amandin.

Jin, T., Albillos, S.M., Guo, F., Howard, A., Fu, T.J., Kothary, M.H., Zhang, Y.Z.

(2009) J Agric Food Chem 57: 8643-8651

• PubMed: 19694440 
• DOI: 10.1021/jf9017355
• Primary Citation of Related Structures:  
  3FZ3


• PubMed Abstract: 
  

Seed storage proteins are accumulated during seed development and act as a reserve of nutrition for seed germination and young sprout growth. Plant seeds play an important role in human nutrition by providing a relatively inexpensive source of protein. However, many plant foods contain allergenic proteins, and the number of people suffering from food allergies has increased rapidly in recent years. The 11S globulins are the most widespread seed storage proteins, present in monocotyledonous and dicotyledonous seeds as well as in gymnosperms (conifers) and other spermatophytes. This family of proteins accounts for a number of known major food allergens. They are of interest to both the public and industry due to food safety concerns. Because of the interests in the structural basis of the allergenicity of food allergens, we sought to determine the crystal structure of Pru1, the major component of the 11 S storage protein from almonds. The structure was refined to 2.4 A, and the R/Rfree for the final refined structure is 17.2/22.9. Pru1 is a hexamer made of two trimers. Most of the back-to-back trimer-trimer association was contributed by monomer-monomer interactions. An alpha helix (helix 6) at the C-terminal end of the acidic domain of one of the interacting monomers lies at the cleft of the two protomers. The residues in this helix correspond to a flexible region in the peanut allergen Ara h 3 that encompasses a previously defined linear IgE epitope.

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Organizational Affiliation: 

Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prunin	A, B, C, D, E, F	531	Prunus dulcis	Mutation(s): 0
Find proteins for Q43607 (Prunus dulcis) Explore Q43607  Go to UniProtKB:  Q43607

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A, B, C, D, E, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	A, B, C, D, E, F	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.229 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.021	α = 90
b = 151.021	β = 90
c = 165.367	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-23 
• Released Date: 2009-11-10 
Deposition Author(s): Jin, T.C., Zhang, Y.Z.

Revision History 

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description