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- PDB-9h1u: Cryo-EM structure of Heterooligomeric Bacterioferritin -

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Basic information

Entry
Database: PDB / ID: 9h1u
TitleCryo-EM structure of Heterooligomeric Bacterioferritin
Components(Bacterioferritin) x 3
KeywordsMETAL BINDING PROTEIN / Heterooligomer / Iron-storage protein / Heme binding / Octahedral
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
: / PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin / Bacterioferritin
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsStein, D. / Zalk, R. / Shahar, A. / Zarivach, R. / Frank, G.A.
Funding support Israel, 1items
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, T.C.T. / Zalk, R. / Shahar, A. / Uebe, R. / Zarivach, R. / Frank, A.G.
History
DepositionOct 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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)425,29744
Polymers421,93824
Non-polymers3,35920
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
Bacterioferritin


Mass: 18213.979 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Gene: bfr, MGMSRv2__3703
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V6F8F5
#2: Protein
Bacterioferritin


Mass: 15412.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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".
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Protein
Bacterioferritin


Mass: 17881.363 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Gene: MGR_0532
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6NE81
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe / 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: Bacterioferritin / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrizamaTris-HCl1
2500 mMSodium ChlorideNaCl1
3500 mMImidazoleImidazole1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239662 / Symmetry type: POINT

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