5XND | pdb_00005xnd

Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel

• PDB DOI: https://doi.org/10.2210/pdb5XND/pdb
• BMRB: 36086

• Classification: METAL BINDING PROTEIN
• Organism(s): Scomber japonicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-22 Released: 2017-12-27 
• Deposition Author(s): Kumeta, H., Nakayama, H., Ogura, K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel

Kumeta, H., Nakayama, H., Ogura, K.

(2017) Sci Rep 7: 17160-17160

• PubMed: 29215073 
• DOI: https://doi.org/10.1038/s41598-017-17281-6
• Primary Citation Related Structures: 
  5XND


• PubMed Abstract: 
  

  Although fish is an important part of the human diet, it is also a common source of food allergy. The major allergen in fish is parvalbumin, a well-conserved Ca ²⁺ -binding protein found in the white muscle of many fish species. Here, we studied the solution structure of the parvalbumin Sco j 1, derived from the Pacific mackerel, using nuclear magnetic resonance spectroscopy. We mapped the IgE-binding epitope proposed in a recent study onto the present structure. Interestingly, three of four residues, which were elucidated as key residues of the IgE-binding epitope, were exposed to solvent, whereas one residue faced the inside of the molecule. We expect that this solution structure can be used in future studies attempting to analyze the various IgE-binding modes of these allergens.

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Organizational Affiliation: 
• Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 21 Nishi 11, Kita, Sapporo, 0110021, Japan.
Laboratory of Biomolecular Functionalities, Department of Food Science, Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 9218836, Japan.
Laboratory of Biomolecular Functionalities, Department of Food Science, Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 9218836, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 12.05 kDa 
• Atom Count: 818 
• Modeled Residue Count: 110 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parvalbumin beta	A	114	Scomber japonicus	Mutation(s): 0
UniProt
Find proteins for P59747 (Scomber japonicus) Explore P59747  Go to UniProtKB:  P59747

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Kumeta, H., Nakayama, H., Ogura, K.

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references