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- EMDB-51772: Cryo-EM structure of Heterooligomeric Bacterioferritin -

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Basic information

Entry
Database: EMDB / ID: EMD-51772
TitleCryo-EM structure of Heterooligomeric Bacterioferritin
Map data
Sample
  • Complex: Bacterioferritin
    • Protein or peptide: Bacterioferritin
    • Protein or peptide: Bacterioferritin
    • Protein or peptide: Bacterioferritin
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FE (III) ION
KeywordsHeterooligomer / Iron-storage protein / Heme binding / Octahedral / METAL BINDING PROTEIN
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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 speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsStein D / Zalk R / Shahar A / Zarivach R / Frank GA
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation163/22 Israel
CitationJournal: To Be Published
Title: THE NEGATIVE DESIGN PRINCIPLES OF HETERO-OLIGOMERIC FERRITIN REVEALED BY CRYO-EM AND GRAPH-THEORY ANALYSIS
Authors: Stein D / Jartoux B / Dror S / Koubkova-Yu TCT / Zalk R / Shahar A / Uebe R / Zarivach R / Frank AG
History
DepositionOct 10, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51772.png

Downloads & links

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Map

FileDownload / File: emd_51772.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.14697261 - 0.24488471
Average (Standard dev.)-0.0000010868788 (±0.016593326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51772_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51772_half_map_2.map
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
    • Protein or peptide: Bacterioferritin
    • Protein or peptide: Bacterioferritin
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FE (III) ION

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Supramolecule #1: Bacterioferritin

SupramoleculeName: Bacterioferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Molecular weightTheoretical: 18.213979 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MKANRTVLAA LNDVLRHQLT AINQYFLHAR MMKNWGFNAL GKHEYKESIE EMKAADKLIE RILLLEGLPN LQDLGKLLIG ENVPEMLKN DFAMEKDAHA DLVKTIALCE KQADYVSRDL LSEFLEECEE RMDFYETQLE LVKKMGEQNY LQSAVGALE

UniProtKB: Bacterioferritin

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Macromolecule #2: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 2
Details: The densities of chains I-L are an average of both Bfr1 and Bfr2, positions where they differ in their sequence (91 out of 159 positions) were changed to Alanine with the residue name "unknown".
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Molecular weightTheoretical: 15.412395 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)V(UNK)(UNK)(UNK) LN(UNK)(UNK)L(UNK)(UNK)(UNK)LT A (UNK)(UNK)QYF(UNK)HA RM(UNK)(UNK)NWGF(UNK)(UNK) L(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)E (UNK) (UNK)(UNK)E(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)V(UNK)(UNK)(UNK) LN(UNK)(UNK)L(UNK)(UNK)(UNK)LT A (UNK)(UNK)QYF(UNK)HA RM(UNK)(UNK)NWGF(UNK)(UNK) L(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)E (UNK) (UNK)(UNK)E(UNK)(UNK)(UNK)A(UNK)(UNK)L I(UNK)RIL(UNK)LEG(UNK) P(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)L (UNK)IG(UNK)(UNK)VP(UNK)M(UNK) (UNK)ND(UNK)A(UNK)E(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)L(UNK)(UNK)(UNK)IA LCE(UNK)(UNK)(UNK)DY(UNK)(UNK) R(UNK) (UNK)L(UNK)(UNK)(UNK)LE E(UNK)E(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)L (UNK)V(UNK)(UNK)G (UNK)(UNK)D(UNK) L(UNK)(UNK)KNYLQS(UNK) A(UNK)(UNK)(UNK)

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Macromolecule #3: Bacterioferritin

MacromoleculeName: Bacterioferritin / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Molecular weightTheoretical: 17.881363 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
PRGSPKVISV LNGLLTGELT AADQYFVHAR MLENWGFKVL YERIEHERHD ELDHAGLLIN RILFLEGVPD VASRAALNIG SDVPKMMAN DLAYELQVVD ELKAAIALCE SERDYDTRRI LVHLLEETEQ DHVRWLEVQV GLIDKLGLKN YLQSAAGEI

UniProtKB: Bacterioferritin

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

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

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 16 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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
Component:
ConcentrationFormulaName
50.0 mMTris-HClTrizama
500.0 mMNaClSodium Chloride
500.0 mMImidazoleImidazole
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3r2h


Details: Additional PDB model was used: 4TOF
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239662
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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