[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleBacterioferritin nanocage structures uncover the biomineralization process in ferritins.
Journal, issue, pagesPNAS Nexus, Vol. 2, Issue 7, Page pgad235, Year 2023
Publish dateJul 20, 2023
AuthorsChacko Jobichen / Tan Ying Chong / Rajesh Rattinam / Sandip Basak / Mahalashmi Srinivasan / Yeu Khai Choong / Kannu Priya Pandey / Tran Bich Ngoc / Jian Shi / Jayaraman Angayarkanni / J Sivaraman /
PubMed AbstractIron 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 ...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.
External linksPNAS Nexus / PubMed:37529551 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 5.8 Å
Structure data

33639

7y6f

EMDB-33639, PDB-7y6f:
Cryo-EM structure of Apo form of ScBfr
Method: EM (single particle) / Resolution: 2.7 Å

33640

7y6g

EMDB-33640, PDB-7y6g:
Cryo-EM structure of bacterioferritin holoform 1a
Method: EM (single particle) / Resolution: 3.6 Å

33645

7y6p

EMDB-33645, PDB-7y6p:
Cryo-EM structure if bacterioferritin holoform
Method: EM (single particle) / Resolution: 3.3 Å

36137

8jax

EMDB-36137, PDB-8jax:
Cryo-EM structure of Holo form of ScBfr with O symmetry
Method: EM (single particle) / Resolution: 3.27 Å

36139

8jb0

EMDB-36139, PDB-8jb0:
Cryo-EM structure of Holo form of ScBfr in C1 symmetry
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-36140: Cryo-EM structure of Fe-biomineral from bacterioferritin
Method: EM (single particle) / Resolution: 5.8 Å

Chemicals

ChemComp-FE2:
Unknown entry

ChemComp-FE:
Unknown entry / Iron

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

Source
  • streptomyces coelicolor (bacteria)
KeywordsMETAL BINDING PROTEIN / Bacterioferritin / OXIDOREDUCTASE

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more