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- EMDB-33645: Cryo-EM structure if bacterioferritin holoform -

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Basic information

Entry
Database: EMDB / ID: EMD-33645
TitleCryo-EM structure if bacterioferritin holoform
Map dataFinal Map
Sample
  • Complex: Bacterioferritin
    • Protein or peptide: Bacterioferritin
  • Ligand: FE (II) ION
  • Ligand: FE (III) ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsBacterioferritin / METAL 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
Biological speciesStreptomyces coelicolor (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJobichen C / Sivaraman J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PNAS Nexus / Year: 2023
Title: Bacterioferritin nanocage structures uncover the biomineralization process in ferritins.
Authors: Chacko Jobichen / Tan Ying Chong / Rajesh Rattinam / Sandip Basak / Mahalashmi Srinivasan / Yeu Khai Choong / Kannu Priya Pandey / Tran Bich Ngoc / Jian Shi / Jayaraman Angayarkanni / J Sivaraman /
Abstract: Iron is an essential element involved in various metabolic processes. The ferritin family of proteins forms nanocage assembly and is involved in iron oxidation, storage, and mineralization. Although ...Iron is an essential element involved in various metabolic processes. The ferritin family of proteins forms nanocage assembly and is involved in iron oxidation, storage, and mineralization. Although several structures of human ferritins and bacterioferritins have been solved, there is still no complete structure that shows both the trapped Fe-biomineral cluster and the nanocage. Furthermore, whereas the mechanism of iron trafficking has been explained using various approaches, structural details on the biomineralization process (i.e. the formation of the mineral itself) are generally lacking. Here, we report the cryo-electron microscopy (cryo-EM) structures of apoform and biomineral bound form (holoforms) of the bacterioferritin (ScBfr) nanocage and the subunit crystal structure. The holoforms show different stages of Fe-biomineral accumulation inside the nanocage, in which the connections exist in two of the fourfold channels of the nanocage between the C-terminal of the ScBfr monomers and the Fe-biomineral cluster. The mutation and truncation of the bacterioferritin residues involved in these connections significantly reduced the iron and phosphate binding in comparison with those of the wild type and together explain the underlying mechanism. Collectively, our results represent a prototype for the bacterioferritin nanocage, which reveals insight into its biomineralization and the potential channel for bacterioferritin-associated iron trafficking.
History
DepositionJun 21, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33645.png

Downloads & links

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Map

FileDownload / File: emd_33645.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0212
Minimum - Maximum-0.07113971 - 0.1293933
Average (Standard dev.)0.00028433735 (±0.008571627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 2

Fileemd_33645_half_map_1.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_33645_half_map_2.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterioferritin

EntireName: Bacterioferritin
Components
  • Complex: Bacterioferritin
    • Protein or peptide: Bacterioferritin
  • Ligand: FE (II) ION
  • Ligand: FE (III) ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Bacterioferritin

SupramoleculeName: Bacterioferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces coelicolor (bacteria)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145
Molecular weightTheoretical: 18.434775 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MQGDPEVIEF LNEQLTAELT AINQYFLHAK LQDHKGWTKL AKYTRAESFD EMRHAEVLTD RILLLDGLPN YQRLFHVRVG QSVTEMFQA DREVELEAID RLRRGIEVMR AKHDITSANV FEAILADEEH HIDYLETQLD LIEKLGESLY LSTVIEQTQ

UniProtKB: Bacterioferritin

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Macromolecule #2: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 12 / 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

Concentration1.8 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
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: PDB ENTRY
PDB model - PDB ID:

5xx9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8174
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

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