9X0L | pdb_00009x0l

Cryo-EM Structure of Turbo sazae ferritin chain B

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

  • Deposited: 2025-09-30 Released: 2026-06-03 
  • Deposition Author(s): Namikawa, Y., Suzuki, M.
  • Funding Organization(s): Japan Society for the Promotion of Science (JSPS), New Energy and Industrial Technology Development Organization (NEDO)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Identification, functional characterization, and cryo-EM structural analysis of novel ferritin subunits in Turbo sazae.

Namikawa, Y.Negishi, L.Kurumizaka, H.Suzuki, M.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70601
  • Primary Citation Related Structures: 
    9X0K, 9X0L

  • PubMed Abstract: 

    Turbo sazae, an edible gastropod, accumulates high levels of iron in its digestive gland, and the molecular mechanism underlying this accumulation has remained elusive. This study identified the proteins responsible for the iron accumulation and characterized their function and structure. We isolated two novel ferritins, TsFerA and TsFerB, from the digestive gland using high-performance liquid chromatography and inductively coupled plasma mass spectrometry. Gene expression analyses revealed that both genes were specifically expressed in the digestive gland. Recombinant TsFerA (rTsFerA) possessed ferroxidase (EC1.16.3.1) activity, whereas recombinant TsFerB (rTsFerB) showed no such activity. This result indicated that rTsFerA functions as an H-chain-like subunit responsible for iron oxidation, while rTsFerB acts as an L-chain-like subunit involved in iron core nucleation. Furthermore, we determined the structures of rTsFerA and rTsFerB using cryo-electron microscopy, at a resolution of 2.19 and 2.17 Å, respectively. The protein structures revealed a conserved ferroxidase center in rTsFerA, whereas key catalytic residues were substituted in rTsFerB. These findings demonstrate that T. sazae utilizes a cooperative system composed of two functionally distinct ferritin subunits to efficiently and safely store iron. This work clarifies the molecular mechanisms of iron metabolism in marine organisms, particularly in gastropods, revealing an optimized strategy to cope with massive iron influx.


  • Organizational Affiliation
    • Laboratory of Analytical Chemistry, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 478.38 kDa 
  • Atom Count: 33,336 
  • Modeled Residue Count: 4,080 
  • Deposited Residue Count: 4,104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TsFerB171Turbo sazaeMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.2
MODEL REFINEMENTPHENIX1.21.2-5419

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP19H05771
Japan Society for the Promotion of Science (JSPS)JapanJP19H05775
Japan Society for the Promotion of Science (JSPS)JapanJP23H00339
Japan Society for the Promotion of Science (JSPS)JapanJP24KJ0914
New Energy and Industrial Technology Development Organization (NEDO)JapanJPNP22100161-0

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release