4M9W | pdb_00004m9w

Crystal Structure of Ara h 8 with MES bound

• PDB DOI: https://doi.org/10.2210/pdb4M9W/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arachis hypogaea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-15 Released: 2013-11-27 
• Deposition Author(s): Offermann, L.R., Hurlburt, B.K., Majorek, K.A., McBride, J.K., Maleki, S.J., Chruszcz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of the Peanut Panallergen Ara h 8.

Hurlburt, B.K., Offermann, L.R., McBride, J.K., Majorek, K.A., Maleki, S.J., Chruszcz, M.

(2013) J Biological Chem 288: 36890-36901

• PubMed: 24253038 
• DOI: https://doi.org/10.1074/jbc.M113.517797
• Primary Citation Related Structures: 
  4M9B, 4M9W, 4MA6, 4MAP


• PubMed Abstract: 
  

  The incidence of peanut allergy continues to rise in the United States and Europe. Whereas exposure to the major allergens Ara h 1, 2, 3, and 6 can cause fatal anaphylaxis, exposure to the minor allergens usually does not. Ara h 8 is a minor allergen. Importantly, it is the minor food allergens that are thought to be responsible for oral allergy syndrome (OAS), in which sensitization to airborne allergens causes a Type 2 allergic reaction to ingested foods. Furthermore, it is believed that similar protein structure rather than a similar linear sequence is the cause of OAS. Bet v 1 from birch pollen is a common sensitizing agent, and OAS results when patients consume certain fruits, vegetables, tree nuts, and peanuts. Here, we report the three-dimensional structure of Ara h 8, a Bet v 1 homolog. The overall fold is very similar to that of Bet v 1, Api g 1 (celery), Gly m 4 (soy), and Pru av 1 (cherry). Ara h 8 binds the isoflavones quercetin and apigenin as well as resveratrol avidly.

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Organizational Affiliation: 
• From the Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, Louisiana 70124.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.19 kDa 
• Atom Count: 2,513 
• Modeled Residue Count: 312 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ara h 8 allergen	A, B	157	Arachis hypogaea	Mutation(s): 0
UniProt
Find proteins for Q6VT83 (Arachis hypogaea) Explore Q6VT83  Go to UniProtKB:  Q6VT83

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
NA	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.183	α = 90
b = 87.488	β = 95.84
c = 42.29	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Offermann, L.R., Hurlburt, B.K., Majorek, K.A., McBride, J.K., Maleki, S.J., Chruszcz, M.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description