4X9U | pdb_00004x9u

Crystal structure of the kiwifruit allergen Act d 5

• PDB DOI: https://doi.org/10.2210/pdb4X9U/pdb

• Classification: PLANT PROTEIN
• Organism(s): Actinidia deliciosa
• Mutation(s): Yes 


• Deposited: 2014-12-11 Released: 2015-07-29 
• Deposition Author(s): Offermann, L.R., Perdue, M.L., Giangrieco, I., Tamburrini, M., Ciardiello, M.A., Chruszcz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Elusive Structural, Functional, and Immunological Features of Act d 5, the Green Kiwifruit Kiwellin.

Offermann, L.R., Giangrieco, I., Perdue, M.L., Zuzzi, S., Santoro, M., Tamburrini, M., Cosgrove, D.J., Mari, A., Ciardiello, M.A., Chruszcz, M.

(2015) J Agric Food Chem 63: 6567-6576

• PubMed: 26146952 
• DOI: https://doi.org/10.1021/acs.jafc.5b02159
• Primary Citation Related Structures: 
  4X9U


• PubMed Abstract: 
  

  Kiwellin (Act d 5) is an allergenic protein contained in kiwifruit pulp in high amounts. The aim of this study was to investigate the three-dimensional structure of the natural molecule from green kiwifruit and its possible function. Kiwellin was crystallized, and its structure, including post-translational modifications, was elucidated. The molecular weight and structural features, in solution, were analyzed by gel filtration and circular dichroism, respectively. Although structurally similar to expansin, kiwellin lacks expansin activity and carbohydrate binding. A specific algorithm was applied to investigate any possible IgE reactivity correlation between kiwellin and a panel of 102 allergens, including expansins and other carbohydrate-binding allergens. The available data suggest a strong dependence of the kiwellin structure on the environmental/experimental conditions. This dependence therefore poses challenges in detecting the correlations between structural, functional, and immunological features of this protein.

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Organizational Affiliation: 
• †Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States.
§Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, I-80131 Napoli, Italy.
#Center for Molecular Allergology, IDI-IRCCS, Rome, Italy.
ΔAssociated Centers for Molecular Allergology, Rome and Latium, Italy.
⊥Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.83 kDa 
• Atom Count: 2,571 
• Modeled Residue Count: 326 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kiwellin	A, B	189	Actinidia deliciosa	Mutation(s): 1
UniProt
Find proteins for P84527 (Actinidia deliciosa) Explore P84527  Go to UniProtKB:  P84527

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PXU	A, B	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.392	α = 90
b = 60.417	β = 95.85
c = 55.601	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Offermann, L.R., Perdue, M.L., Giangrieco, I., Tamburrini, M., Ciardiello, M.A., Chruszcz, M.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection