8UAI | pdb_00008uai

Crystal structure of hetero hexameric hazelnut allergen Cor a 9

  • Classification: ALLERGEN
  • Organism(s): Corylus avellana
  • Mutation(s): No 

  • Deposited: 2023-09-21 Released: 2024-05-15 
  • Deposition Author(s): Zhang, Y.Z., Guo, F.
  • Funding Organization(s): United States Department of Agriculture (USDA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8UAI

This is version 1.1 of the entry. See complete history

Literature

Crystal structure of hetero hexameric 11S seed storage protein of hazelnut.

Guo, F.Zhang, Y.Howard, A.Xu, Y.

(2024) Plant Physiol Biochem 210: 108653-108653

  • DOI: https://doi.org/10.1016/j.plaphy.2024.108653
  • Primary Citation Related Structures: 
    8UAI

  • PubMed Abstract: 

    Edible plant seeds provide a relatively inexpensive source of protein and make up a large part of nutrients for humans. Plant seeds accumulate storage proteins during seed development. Seed storage proteins act as a reserve of nutrition for seed germination and seedling growth. However, seed storage proteins may be allergenic, and the prevalence of food allergy has increased rapidly in recent years. The 11S globulins account for a significant number of known major food allergens. They are of interest to the public and the agricultural industry because of food safety concerns and the need for crop enhancement. We sought to determine the crystal structure of Cor a 9, the 11 S storage protein of hazelnut and a food allergen. The structure was refined to 1.92 Å, and the R and R free for the refined structure are 17.6% and 22.5%, respectively. The structure of Cor a 9 showed a hetero hexamer of an 11S seed storage protein for the first time. The hexamer was two trimers associated back-to-back. Two long alpha helixes at the C-terminal end of the acidic domain of one of the Cor a 9 isoforms lay at the trimer-trimer interface's groove. These data provided much-needed information about the allergenicity of the 11S seed proteins. The information may also facilitate a better understanding of the folding and transportation of 11S seed storage proteins.


  • Organizational Affiliation
    • Discover Biotherapeutics, Exelixis Inc. 1851 Harbor Bay Parkway, Alameda, CA 94502, USA.

Macromolecule Content 

  • Total Structure Weight: 340.49 kDa 
  • Atom Count: 20,255 
  • Modeled Residue Count: 2,405 
  • Deposited Residue Count: 2,960 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
11S globulin 1
A, D
493Corylus avellanaMutation(s): 0 
UniProt
Find proteins for Q8W1C2 (Corylus avellana)
Explore Q8W1C2 
Go to UniProtKB:  Q8W1C2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8W1C2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
11S globulin 2
B, E
494Corylus avellanaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
11S globulin 3
C, F
493Corylus avellanaMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth E],
R [auth E],
S [auth E],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
L [auth B],
O [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.168α = 90
b = 91.093β = 90.32
c = 74.854γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States Department of Agriculture (USDA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary