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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: Proc Natl Acad Sci U S A / Year: 2026
Title: The assembly rules guiding hetero-oligomeric bacterioferritin organization and their evolutionary signature.
Authors: Daniel Stein / Bruno Jartoux / Shiran Dror / René Uebe / Tracy Chih-Ting Koubková-Yu / Ran Zalk / Anat Shahar / Raz Zarivach / Gabriel A Frank /
Abstract: Homomeric and heteromeric protein complexes are ubiquitous across all domains of life. The evolutionary transition from homo- to hetero-oligomers by gene duplication and chain specialization is ...Homomeric and heteromeric protein complexes are ubiquitous across all domains of life. The evolutionary transition from homo- to hetero-oligomers by gene duplication and chain specialization is widespread, yet it entails challenging requirements for maintaining oligomerization and functionality. Chain specialization in ferritins, which occurs in bacteria, vertebrates, and plants, is a salient example of this phenomenon. In heteroferritins, the two essential functions, ferroxidase activity and electron transfer, are split between two specialized chain types. Many heteroferritins assemble into complexes with variable subunit ratios, implying the existence of assembly rules that balance compositional flexibility with structural constraints. Here, we identify the assembly rules governing the organization of the heterobacterioferritin from (MSR-1 Bfr) by analyzing its cryo-EM reconstructions. These rules consist of structural constraints that limit the number of possible arrangements and promote juxtaposition of the two, now separated functions. These constraints support compositional flexibility while preserving function, thereby providing resilience to stochastic variation in oligomer stoichiometry. Bioinformatic analysis revealed that the assembly rules identified in MSR-1 Bfr are widespread across the Bfr family and coevolved with chain specialization. Together, these findings support leading models of hetero-oligomer evolution and reveal the emergence of order-exerting mutations that shape the organization of multimeric protein complexes while conserving function.
History
DepositionOct 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: 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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