9IIG | pdb_00009iig

Cryo-EM structure of hetero-bacterioferritin SoBfr12 from Shewanella oneidensis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unveiling Structural Heterogeneity and Evolutionary Adaptations of Heteromultimeric Bacterioferritin Nanocages.

Li, Y.Wang, W.Wang, W.Zhang, X.Chen, J.Gao, H.

(2025) Adv Sci (Weinh) 12: e2409957-e2409957

  • DOI: https://doi.org/10.1002/advs.202409957
  • Primary Citation of Related Structures:  
    9IIG

  • PubMed Abstract: 

    Iron-storage bacterioferritins (Bfrs), existing in either homo- or hetero-multimeric form, play a crucial role in iron homeostasis. While the structure and function of homo-multimeric bacterioferritins (homo-Bfrs) have been extensively studied, little is known about the assembly, distinctive characteristics, or evolutionary adaptations of hetero-multimeric bacterioferritins (hetero-Bfrs). Here, the cryo-EM structure and functional characterization of a bacterial hetero-Bfr (SoBfr12) are reported. Compared to homo-Bfrs, although SoBfr12 exhibits a conserved spherical cage-like dodecahedron, its pores through which ions traverse exhibit substantially increased diversity. Importantly, the heterogeneity has significant impacts on sites for ion entry, iron oxidation, and reduction. Moreover, evolutionary analyses reveal that hetero-Bfrs may represent a new class within the Bfr subfamily, consisting of two different types that may have evolved from homo-Bfr through tandem duplication and directly from ferritin (Ftn) via dispersed duplication, respectively. These results reveal remarkable structural and functional features of a hetero-Bfr, enabling the rational design of nanocages for enhanced iron-storing efficiency and for other specific purposes, such as drug delivery vehicles and nanozymes.


  • Organizational Affiliation
    • State Key Laboratory for Vegetation Structure, Function and Construction (VegLab), Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterioferritin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
155Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: brf1SO_1112
EC: 1.16.3.1
UniProt
Find proteins for Q8EHV0 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EHV0 
Go to UniProtKB:  Q8EHV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EHV0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterioferritin
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
157Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: brf2SO_1111
EC: 1.16.3.1
UniProt
Find proteins for Q8EHV1 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EHV1 
Go to UniProtKB:  Q8EHV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EHV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
EA [auth N]
FA [auth O]
GA [auth Q]
HA [auth S]
IA [auth U]
EA [auth N],
FA [auth O],
GA [auth Q],
HA [auth S],
IA [auth U],
JA [auth X]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth D]
CA [auth G]
DA [auth K]
Y [auth A]
AA [auth C],
BA [auth D],
CA [auth G],
DA [auth K],
Y [auth A],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930003

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-18
    Changes: Data collection, Database references