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- EMDB-60594: Cryo-EM structure of hetero-bacterioferritin SoBfr12 from Shewane... -

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Basic information

Entry
Database: EMDB / ID: EMD-60594
TitleCryo-EM structure of hetero-bacterioferritin SoBfr12 from Shewanella oneidensis
Map data
Sample
  • Complex: Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr12 in C1 symmetry
    • Protein or peptide: Bacterioferritin
    • Protein or peptide: Bacterioferritin
  • Ligand: SODIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
Keywords24-mer bacterioferritin / metal transport / oxidoreductase / heme-binding protein
Function / homology
Function and homology information


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
Bacterioferritin / Bacterioferritin
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGao HC / Chen JH / Li YX
Funding support China, 1 items
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, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60594.png

Downloads & links

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Map

FileDownload / File: emd_60594.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.47 Å/pix.
x 440 pix.
= 204.6 Å		0.47 Å/pix.
x 440 pix.
= 204.6 Å		0.47 Å/pix.
x 440 pix.
= 204.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.465 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.323005 - 0.8501598
Average (Standard dev.)0.0009335122 (±0.026441565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 204.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_60594_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_60594_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr...

EntireName: Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr12 in C1 symmetry
Components
  • Complex: Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr12 in C1 symmetry
    • Protein or peptide: Bacterioferritin
    • Protein or peptide: Bacterioferritin
  • Ligand: SODIUM ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr...

SupramoleculeName: Cryo-EM structure of Shewanelle oneidensis bacterioferritin SoBfr12 in C1 symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)

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Macromolecule #1: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 17.997393 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKGDKDVIDA LNRLLTGELS AMDQYFVHAH MYEDWGLNEL YERIAHESDD EKGHAAKLVQ RILFLEGVPN VAAREALNIG SNVEEMLRN DLAYEYKVAD DLRKVIALCE QKKDYQTREI LEVLLDDTES DHMYWLEKQL GLIDRIGLAN YLQTKM

UniProtKB: Bacterioferritin

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Macromolecule #2: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 18.408 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKGHPKVVGQ LNRVLTCELT AINQYFLHAR MFKHWGLEKL NHVEYKKSIE DMKHADKLIE RVLFLEGLPN LQQLEKLRIG EHAQEMLDC DLAMVQEQLT LLRDAITLCE AEQDYVSRDL LEDILEDEEE HLDWLESQRE LIGLTGIQNY LQSQISES

UniProtKB: Bacterioferritin

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 6
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 6940 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: alphafold3.0
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 736353
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)

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