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

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Basic information

Entry
Database: PDB / ID: 9x0l
TitleCryo-EM Structure of Turbo sazae ferritin chain B
ComponentsTsFerB
KeywordsMETAL BINDING PROTEIN / Apoferritin / Iron / Storage / 24-mer / Metal Binding
Biological speciesTurbo sazae (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsNamikawa, Y. / Suzuki, M.
Funding support Japan, 5items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TsFerB
B: TsFerB
C: TsFerB
D: TsFerB
E: TsFerB
F: TsFerB
G: TsFerB
H: TsFerB
I: TsFerB
J: TsFerB
K: TsFerB
L: TsFerB
M: TsFerB
N: TsFerB
O: TsFerB
P: TsFerB
Q: TsFerB
R: TsFerB
S: TsFerB
T: TsFerB
V: TsFerB
W: TsFerB
X: TsFerB
Y: TsFerB


Theoretical massNumber of molelcules
Total (without water)478,38324
Polymers478,38324
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
TsFerB


Mass: 19932.641 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Details: DDBJ accession number: LC893404 / Source: (gene. exp.) Turbo sazae (invertebrata) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ferritin chain B of Turbo sazae / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Turbo sazae (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethane-hydrogen chlorideTris-HCl1
2200 mMsodium chlorideNaCl1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
7Coot0.9.6.2model fitting
12cryoSPARC4.6.23D reconstruction
13PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30685 / Symmetry type: POINT
Atomic model buildingB value: 59.88 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: stereochemistry
Atomic model buildingDetails: phenix.map_to_model / Source name: Other / Type: in silico model

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