3FZ3

Crystal Structure of almond Pru1 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/jf9017355

  • 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 protei ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prunin
A, B, C, D, E, F
531Prunus dulcisMutation(s): 0 
Gene Names: pru1
Find proteins for Q43607 (Prunus dulcis)
Go to UniProtKB:  Q43607
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 151.021α = 90.00
b = 151.021β = 90.00
c = 165.367γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description