5E1R

Crystal structure of pecan (carya illinoinensis) vicilin, a new food allergen

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report



Literature

Identification and Characterization of a New Pecan [Carya illinoinensis (Wangenh.) K. Koch] Allergen, Car i 2.

Zhang, Y., Lee, B., Du, W.X., Lyu, S.C., Nadeau, K.C., Grauke, L.J., Zhang, Y., Wang, S., Fan, Y., Yi, J., McHugh, T.H.

(2016) J Agric Food Chem 64: 4146-4151

  • DOI: 10.1021/acs.jafc.6b00884
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The 7S vicilin and 11S legumin seed storage globulins belong to the cupin protein superfamily and are major food allergens in many foods from the "big eight" food allergen groups. Here, for the first time, pecan vicilin was found to be a food allerge ...

    The 7S vicilin and 11S legumin seed storage globulins belong to the cupin protein superfamily and are major food allergens in many foods from the "big eight" food allergen groups. Here, for the first time, pecan vicilin was found to be a food allergen. Western blot experiments revealed that 30% of 27 sera used in this study and 24% of the sera from 25 patients with double-blind, placebo controlled clinical pecan allergy contained IgE antibodies specific to pecan vicilin. This allergen consists of a low-complexity region at its N-terminal and a structured domain at the C-terminal that contains two cupin motifs and forms homotrimers. The crystal structure of recombinant pecan vicilin was determined. The refined structure gave R/Rfree values of 0.218/0.262 for all data to 2.65 Å. There were two trimeric biological units in the crystallographic asymmetric unit. Pecan vicilin is also a copper protein. These data may facilitate the understanding of the nutritional value and the allergenicity relevance of the copper binding property of seed storage proteins in tree nuts.

    Organizational Affiliation: 

    Western Regional Research Center, Pacific West Area, Agricultural Research Service, U.S. Department of Agriculture , 800 Buchanan Street, Albany, California 94710, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7S vicilin
A, B, C, D, E, F
426Carya illinoinensisMutation(s): 0 
Gene Names: pec2a1a, pec3a1a, pec4a1a
Find proteins for B3STU4 (Carya illinoinensis)
Go to UniProtKB:  B3STU4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download CCD File 
A, B, C, D, E, F
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
CU
Query on CU
Download CCD File 
A, B, C, D, E, F
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.691α = 90
b = 151.61β = 90
c = 342.782γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-09-30 
  • Released Date: 2016-08-10 
    • Deposition Author(s): Zhang, Y.Z.

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release