6STA | pdb_00006sta

Crystal structure of the strawberry pathogenesis-related 10 (PR-10) Fra a 1.02 protein, E46A D48A mutant

• PDB DOI: https://doi.org/10.2210/pdb6STA/pdb

• Classification: ALLERGEN
• Organism(s): Fragaria x ananassa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-09-10 Released: 2019-12-18 
• Deposition Author(s): Orozco-Navarrete, B., Kaczmarska, Z., Dupeux, F., Pott, D., Diaz Perales, A., Casanal, A., Marquez, J.A., Valpuesta, V., Merchante, C.
• Funding Organization(s): Ministry of Economy and Competitiveness

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.259 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structural Bases for the Allergenicity of Fra a 1.02 in Strawberry Fruits.

Orozco-Navarrete, B., Kaczmarska, Z., Dupeux, F., Garrido-Arandia, M., Pott, D., Perales, A.D., Casanal, A., Marquez, J.A., Valpuesta, V., Merchante, C.

(2020) J Agric Food Chem 68: 10951-10961

• PubMed: 31774998 
• DOI: https://doi.org/10.1021/acs.jafc.9b05714
• Primary Citation Related Structures: 
  6ST8, 6ST9, 6STA, 6STB


• PubMed Abstract: 
  

  Although strawberries are highly appreciated fruits, their intake can induce allergic reactions in atopic patients. These reactions can be due to the patient's previous sensitization to the major birch pollen allergen Bet v 1, by which IgE generated in response to Bet v 1 cross-reacts with the structurally related strawberry Fra a 1 protein family. Fra a 1.02 is the most expressed paralog in ripe strawberries and is highly allergenic. To better understand the molecular mechanisms regulating this allergic response, we have determined the three-dimensional structure of Fra a 1.02 and four site-directed mutants that were designed based on their positions in potential epitopes. Fra a 1.02 and mutants conform to the START fold. We show that the cross-reactivity of all the mutant variants to IgE from patients allergic to Bet v 1 was significantly reduced without altering the conserved structural fold, so that they could potentially be used as hypoallergenic Fra a 1 variants for the generation of vaccines against strawberry allergy in atopic patients.

---

Organizational Affiliation: 
• Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM), Universidad de Málaga-CSIC, 29016 Málaga, Spain.
European Molecular Biology Laboratory, 38042 Grenoble, France.
International Institute of Molecular and Cell Biology, 12-109 Warsaw, Poland.
Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
Departamento de Biotecnología-Biología Vegetal, Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid, 28040 Madrid, Spain.
Cambridge Biomedical Campus, Francis Crick Avenue, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.24 kDa 
• Atom Count: 2,468 
• Modeled Residue Count: 314 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major strawberry allergen Fra a 1-2	A, B	163	Fragaria x ananassa	Mutation(s): 2  Gene Names: FRAA2
UniProt
Find proteins for D0E0C6 (Fragaria ananassa) Explore D0E0C6  Go to UniProtKB:  D0E0C6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.259 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.138	α = 90
b = 75.433	β = 90
c = 83.109	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Orozco-Navarrete, B., Kaczmarska, Z., Dupeux, F., Pott, D., Diaz Perales, A., Casanal, A., Marquez, J.A., Valpuesta, V., Merchante, C.

---

Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness	Spain	BIO2013-33199-R
Ministry of Economy and Competitiveness	Spain	BES-2014-068723

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2020-10-07
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description