6A4U | pdb_00006a4u

The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin

• PDB DOI: https://doi.org/10.2210/pdb6A4U/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Penaeus japonicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-06-21 Released: 2018-08-22 
• Deposition Author(s): Masuda, T., Mikami, B., Zang, J., Zhao, G.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.157 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

The first crystal structure of crustacean ferritin that is a hybrid type of H and L ferritin

Masuda, T., Zang, J., Zhao, G., Mikami, B.

(2018) Protein Sci 27: 1955-1960

• PubMed: 30099791 
• DOI: https://doi.org/10.1002/pro.3495
• Primary Citation Related Structures: 
  6A4U


• PubMed Abstract: 
  

  Ferritin, a ubiquitous iron storage protein, has a crucial role in innate immunity in arthropods, which have no adaptive immune system. Arthropods are thought to have two types of ferritin molecules: the secreted type and the cytosolic type. Here, we present the first crystal structure of ferritin from crustacean, kuruma prawn (Marsupenaeus japonicus), at 1.16 Å resolution. This shrimp ferritin (MjFer) is the cytosolic type, and its structure shows well-conserved ferritin fold composed of a 4-helix bundle that assembles into a cage-like 24-mer. The structure of MjFer was more similar to those of human and vertebrate ferritins than to that of the secreted-type arthropod ferritin from an insect. MjFer possesses both a ferroxidase site and a nucleation site, which are the main characteristics of vertebrate H and L chain ferritins, respectively. The first crystal structure of crustacean ferritin, MjFer, has exceptionally high quality that provides the detailed structural information of metal moving pathway in ferritin.

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Organizational Affiliation: 
• Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, 611-0011, Japan.
College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing, 100083, China.
Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 120.84 kDa 
• Atom Count: 10,626 
• Modeled Residue Count: 1,014 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C, D, E, F	169	Penaeus japonicus	Mutation(s): 1  EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus) Explore T2B7E1  Go to UniProtKB:  T2B7E1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth B], BA [auth B], LB [auth E], MB [auth E], NA [auth C], P [auth A], Q [auth A], R [auth A], UB [auth F], VA [auth D], VB [auth F], WA [auth D], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AB [auth E], BB [auth E], CB [auth E], DA [auth C], DB [auth E], EA [auth C], EB [auth E], FA [auth C], FB [auth E], G [auth A], GA [auth C], GB [auth E], H [auth A], HA [auth C], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], JB [auth E], K [auth A], KA [auth C], KB [auth E], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NB [auth F], O [auth A], OB [auth F], PB [auth F], QA [auth D], QB [auth F], RA [auth D], RB [auth F], S [auth B], SA [auth D], SB [auth F], T [auth B], TA [auth D], TB [auth F], U [auth B], UA [auth D], V [auth B], W [auth B], X [auth B], Y [auth B], ZA [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	CA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	OA [auth C], PA [auth C], WB [auth F], XA [auth D], YA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.157 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.872	α = 90
b = 124.872	β = 90
c = 175.683	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Masuda, T., Mikami, B., Zang, J., Zhao, G.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP 15K07574

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-11-07
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary