7Y6F

Cryo-EM structure of Apo form of ScBfr

Summary for 7Y6F

• Entry DOI: 10.2210/pdb7y6f/pdb
• EMDB information: 33639
• Descriptor: Bacterioferritin, FE (II) ION, FE (III) ION, ... (4 entities in total)
• Functional Keywords: bacterioferritin, metal binding protein
• Biological source: Streptomyces coelicolor
• Total number of polymer chains: 24
• Total formula weight: 452457.16

Authors

Jobichen, C.,Sivaraman, J. (deposition date: 2022-06-20, release date: 2023-07-05, Last modification date: 2023-09-13)

Primary citation

Jobichen, C.,Ying Chong, T.,Rattinam, R.,Basak, S.,Srinivasan, M.,Choong, Y.K.,Pandey, K.P.,Ngoc, T.B.,Shi, J.,Angayarkanni, J.,Sivaraman, J.
Bacterioferritin nanocage structures uncover the biomineralization process in ferritins.
Pnas Nexus, 2:pgad235-pgad235, 2023

PubMed Abstract: Iron is an essential element involved in various metabolic processes. The ferritin family of proteins forms nanocage assembly and is involved in iron oxidation, storage, and mineralization. Although several structures of human ferritins and bacterioferritins have been solved, there is still no complete structure that shows both the trapped Fe-biomineral cluster and the nanocage. Furthermore, whereas the mechanism of iron trafficking has been explained using various approaches, structural details on the biomineralization process (i.e. the formation of the mineral itself) are generally lacking. Here, we report the cryo-electron microscopy (cryo-EM) structures of apoform and biomineral bound form (holoforms) of the bacterioferritin (ScBfr) nanocage and the subunit crystal structure. The holoforms show different stages of Fe-biomineral accumulation inside the nanocage, in which the connections exist in two of the fourfold channels of the nanocage between the C-terminal of the ScBfr monomers and the Fe-biomineral cluster. The mutation and truncation of the bacterioferritin residues involved in these connections significantly reduced the iron and phosphate binding in comparison with those of the wild type and together explain the underlying mechanism. Collectively, our results represent a prototype for the bacterioferritin nanocage, which reveals insight into its biomineralization and the potential channel for bacterioferritin-associated iron trafficking.

PubMed: 37529551
DOI: 10.1093/pnasnexus/pgad235

Experimental method

ELECTRON MICROSCOPY (2.7 Å)