8JB0

Cryo-EM structure of Holo form of ScBfr in C1 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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

Bacterioferritin nanocage structures uncover the biomineralization process in ferritins.

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.

(2023) PNAS Nexus 2: pgad235-pgad235

  • DOI: https://doi.org/10.1093/pnasnexus/pgad235
  • Primary Citation of Related Structures:  
    7Y6F, 7Y6G, 7Y6P, 8JAX, 8JB0

  • 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 Streptomyces coelicolor 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.


  • Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterioferritin
A,
B,
C,
D,
E [auth F],
F [auth E],
G,
H,
I,
J,
K,
L,
M,
N,
O,
P,
Q,
R,
S,
T,
U,
V,
W,
X
167Streptomyces coelicolorMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for Q9S2N0 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9S2N0 
Go to UniProtKB:  Q9S2N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S2N0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth S]
BA [auth C]
BB [auth T]
CA [auth C]
AA [auth B],
AB [auth S],
BA [auth C],
BB [auth T],
CA [auth C],
CB [auth T],
DA [auth D],
DB [auth U],
EA [auth F],
EB [auth V],
FA [auth E],
FB [auth W],
GA [auth E],
GB [auth W],
HA [auth G],
HB [auth X],
IA [auth G],
JA [auth H],
KA [auth H],
LA [auth I],
MA [auth J],
NA [auth K],
OA [auth K],
PA [auth L],
QA [auth M],
RA [auth M],
SA [auth N],
TA [auth O],
UA [auth O],
VA [auth P],
WA [auth Q],
XA [auth R],
Y [auth A],
YA [auth R],
Z [auth A],
ZA [auth S]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-13
    Changes: Database references