9H1U | pdb_00009h1u

Cryo-EM structure of Heterooligomeric Bacterioferritin

PDB DOI: https://doi.org/10.2210/pdb9H1U/pdb
EM Map EMD-51772: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Magnetospirillum gryphiswaldense MSR-1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-10-10 Released: 2025-10-29
Deposition Author(s): Stein, D., Zalk, R., Shahar, A., Zarivach, R., Frank, G.A.
Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The assembly rules guiding hetero-oligomeric bacterioferritin organization and their evolutionary signature.

Stein, D., Jartoux, B., Dror, S., Uebe, R., Koubkova-Yu, T.C., Zalk, R., Shahar, A., Zarivach, R., Frank, G.A.

(2026) Proc Natl Acad Sci U S A 123: e2504561123-e2504561123

PubMed: 41609675 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2504561123
Primary Citation Related Structures:
9H1U

PubMed 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 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 Magnetospirillum gryphiswaldense (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.

Organizational Affiliation

Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

Macromolecule Content

Total Structure Weight: 425.3 kDa
Atom Count: 29,095
Modeled Residue Count: 3,751
Deposited Residue Count: 3,792
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B, C, D, E A, B, C, D, E, F, G, H	158	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0 Gene Names: bfr, MGMSRv2__3703
UniProt
Find proteins for V6F8F5 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1)) Explore V6F8F5 Go to UniProtKB: V6F8F5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V6F8F5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	I, J, K, L	158	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	158	Magnetospirillum gryphiswaldense MSR-1	Mutation(s): 0 Gene Names: MGR_0532
UniProt
Find proteins for Q6NE81 (Magnetospirillum gryphiswaldense) Explore Q6NE81 Go to UniProtKB: Q6NE81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NE81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth G] SDF format, chain Y [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth G] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth C]	AA [auth E], BA [auth G], Y [auth B], Z [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth G] Focus chain Y [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth G] Focus chain Y [auth B] Focus chain Z [auth C]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain CA [auth M] SDF format, chain DA [auth M] SDF format, chain EA [auth N] SDF format, chain FA [auth N] SDF format, chain GA [auth O] SDF format, chain HA [auth Q] SDF format, chain IA [auth R] SDF format, chain JA [auth T] SDF format, chain KA [auth T] SDF format, chain LA [auth U] SDF format, chain MA [auth V] SDF format, chain NA [auth V] SDF format, chain OA [auth W] SDF format, chain PA [auth W] SDF format, chain QA [auth X] SDF format, chain RA [auth X] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain EA [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth Q] MOL2 format, chain IA [auth R] MOL2 format, chain JA [auth T] MOL2 format, chain KA [auth T] MOL2 format, chain LA [auth U] MOL2 format, chain MA [auth V] MOL2 format, chain NA [auth V] MOL2 format, chain OA [auth W] MOL2 format, chain PA [auth W] MOL2 format, chain QA [auth X] MOL2 format, chain RA [auth X] mmCIF format, chain CA [auth M] mmCIF format, chain DA [auth M] mmCIF format, chain EA [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain GA [auth O] mmCIF format, chain HA [auth Q] mmCIF format, chain IA [auth R] mmCIF format, chain JA [auth T] mmCIF format, chain KA [auth T] mmCIF format, chain LA [auth U] mmCIF format, chain MA [auth V] mmCIF format, chain NA [auth V] mmCIF format, chain OA [auth W] mmCIF format, chain PA [auth W] mmCIF format, chain QA [auth X] mmCIF format, chain RA [auth X]	CA [auth M] DA [auth M] EA [auth N] FA [auth N] GA [auth O] CA [auth M], DA [auth M], EA [auth N], FA [auth N], GA [auth O], HA [auth Q], IA [auth R], JA [auth T], KA [auth T], LA [auth U], MA [auth V], NA [auth V], OA [auth W], PA [auth W], QA [auth X], RA [auth X]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth Q] Focus chain IA [auth R] Focus chain JA [auth T] Focus chain KA [auth T] Focus chain LA [auth U] Focus chain MA [auth V] Focus chain NA [auth V] Focus chain OA [auth W] Focus chain PA [auth W] Focus chain QA [auth X] Focus chain RA [auth X] Interactions & Density Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth Q] Focus chain IA [auth R] Focus chain JA [auth T] Focus chain KA [auth T] Focus chain LA [auth U] Focus chain MA [auth V] Focus chain NA [auth V] Focus chain OA [auth W] Focus chain PA [auth W] Focus chain QA [auth X] Focus chain RA [auth X]