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- PDB-9iig: Cryo-EM structure of hetero-bacterioferritin SoBfr12 from Shewane... -

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Basic information

Entry
Database: PDB / ID: 9iig
TitleCryo-EM structure of hetero-bacterioferritin SoBfr12 from Shewanella oneidensis
Components(Bacterioferritin) x 2
KeywordsOXIDOREDUCTASE / 24-mer bacterioferritin / metal transport / heme-binding protein
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin / Bacterioferritin
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGao, H.C. / Chen, J.H. / Li, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930003 China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Unveiling Structural Heterogeneity and Evolutionary Adaptations of Heteromultimeric Bacterioferritin Nanocages.
Authors: Yingxi Li / Weiwei Wang / Wei Wang / Xing Zhang / Jinghua Chen / Haichun Gao /
Abstract: Iron-storage bacterioferritins (Bfrs), existing in either homo- or hetero-multimeric form, play a crucial role in iron homeostasis. While the structure and function of homo-multimeric ...Iron-storage bacterioferritins (Bfrs), existing in either homo- or hetero-multimeric form, play a crucial role in iron homeostasis. While the structure and function of homo-multimeric bacterioferritins (homo-Bfrs) have been extensively studied, little is known about the assembly, distinctive characteristics, or evolutionary adaptations of hetero-multimeric bacterioferritins (hetero-Bfrs). Here, the cryo-EM structure and functional characterization of a bacterial hetero-Bfr (SoBfr12) are reported. Compared to homo-Bfrs, although SoBfr12 exhibits a conserved spherical cage-like dodecahedron, its pores through which ions traverse exhibit substantially increased diversity. Importantly, the heterogeneity has significant impacts on sites for ion entry, iron oxidation, and reduction. Moreover, evolutionary analyses reveal that hetero-Bfrs may represent a new class within the Bfr subfamily, consisting of two different types that may have evolved from homo-Bfr through tandem duplication and directly from ferritin (Ftn) via dispersed duplication, respectively. These results reveal remarkable structural and functional features of a hetero-Bfr, enabling the rational design of nanocages for enhanced iron-storing efficiency and for other specific purposes, such as drug delivery vehicles and nanozymes.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Jun 18, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)440,70236
Polymers436,86524
Non-polymers3,83712
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Bacterioferritin


Mass: 17997.393 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: brf1, SO_1112 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EHV0, ferroxidase
#2: Protein
Bacterioferritin


Mass: 18408.000 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: brf2, SO_1111 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EHV1, ferroxidase
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr12 in C1 symmetry
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 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 defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6940

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Processing

EM software
IDNameVersionCategory
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
13cryoSPARC4.43D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 736353 / Symmetry type: POINT

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