Crystal Structure of almond Pru1 protein

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/jf9017355
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
531Prunus dulcisMutation(s): 0 
Find proteins for Q43607 (Prunus dulcis)
Explore Q43607 
Go to UniProtKB:  Q43607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43607
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
G [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
S [auth F]
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
K [auth B]
M [auth C]
O [auth D]
H [auth A],
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth E],
T [auth F],
U [auth F]
Experimental Data & Validation

Experimental Data

  • 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 = 151.021α = 90
b = 151.021β = 90
c = 165.367γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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