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- EMDB-66437: Cryo-EM Structure of Turbo sazae ferritin chain B -

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Basic information

Entry
Database: EMDB / ID: EMD-66437
TitleCryo-EM Structure of Turbo sazae ferritin chain B
Map data
Sample
  • Complex: Ferritin chain B of Turbo sazae
    • Protein or peptide: TsFerB
KeywordsApoferritin / Iron / Storage / 24-mer / Metal Binding / METAL BINDING PROTEIN
Biological speciesTurbo sazae (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsNamikawa Y / Suzuki M
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H05771 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05775 Japan
Japan Society for the Promotion of Science (JSPS)JP23H00339 Japan
Japan Society for the Promotion of Science (JSPS)JP24KJ0914 Japan
New Energy and Industrial Technology Development Organization (NEDO)JPNP22100161-0 Japan
CitationJournal: FEBS J / Year: 2026
Title: Identification, functional characterization, and cryo-EM structural analysis of novel ferritin subunits in Turbo sazae.
Authors: Yuto Namikawa / Lumi Negishi / Hitoshi Kurumizaka / Michio Suzuki /
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 ...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.
History
DepositionSep 30, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66437.png

Downloads & links

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Map

FileDownload / File: emd_66437.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 260 pix.
= 130. Å		0.5 Å/pix.
x 260 pix.
= 130. Å		0.5 Å/pix.
x 260 pix.
= 130. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.05988439 - 0.15131171
Average (Standard dev.)-0.00039294153 (±0.020740591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 130.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66437_half_map_1.map
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Half map: #1

Fileemd_66437_half_map_2.map
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Sample components

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Entire : Ferritin chain B of Turbo sazae

EntireName: Ferritin chain B of Turbo sazae
Components
  • Complex: Ferritin chain B of Turbo sazae
    • Protein or peptide: TsFerB

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Supramolecule #1: Ferritin chain B of Turbo sazae

SupramoleculeName: Ferritin chain B of Turbo sazae / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Turbo sazae (invertebrata)

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Macromolecule #1: TsFerB

MacromoleculeName: TsFerB / type: protein_or_peptide / ID: 1 / Details: DDBJ accession number: LC893404 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Turbo sazae (invertebrata)
Molecular weightTheoretical: 19.932641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALSQCRQNF HSDSEGGINK QINILLNASY VYQSMAWYFD RDDVALKGFY EFFKEASNKK REWAECLMKY QNKRGGRIVL QDVKRPSSD EWGTCLDVMM AALTMEKKVN QEFLALHKVA ESKVDPQMTD WIEDEFLEEE VELIKKISDY VTNLKRVGPG L GEYIFDHE TLA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HCltris(hydroxymethyl)aminomethane-hydrogen chloride
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 30685
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: phenix.map_to_model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 59.88 / Target criteria: stereochemistry
Output model

PDB-9x0l:
Cryo-EM Structure of Turbo sazae ferritin chain B

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