Crystal structure of thermotoga maritima E65Q Ferritin

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A single residue can modulate nanocage assembly in salt dependent ferritin.

Kumar, M.Markiewicz-Mizera, J.Janna Olmos, J.D.Wilk, P.Grudnik, P.Biela, A.P.Jemiola-Rzeminska, M.Gorecki, A.Chakraborti, S.Heddle, J.G.

(2021) Nanoscale 13: 11932-11942

  • DOI: https://doi.org/10.1039/d1nr01632f
  • Primary Citation of Related Structures:  
    6TXH, 6TXI, 6TXJ, 6TXK, 6TXL, 6TXM, 6TXN

  • PubMed Abstract: 

    Cage forming proteins have numerous potential applications in biomedicine and biotechnology, where the iron storage ferritin is a widely used example. However, controlling ferritin cage assembly/disassembly remains challenging, typically requiring extreme conditions incompatible with many desirable cargoes, particularly for more fragile biopharmaceuticals. Recently, a ferritin from the hyperthermophile bacterium Thermotoga maritima (TmFtn) has been shown to have reversible assembly under mild conditions, offering greater potential biocompatibility in terms of cargo access and encapsulation. Like Archeoglobus fulgidus ferritin (AfFtn), TmFtn forms 24mer cages mediated by metal ions (Mg2+). We have solved the crystal structure of the wild type TmFtn and several mutants displaying different assembly/disassembly properties. These data combined with other biophysical studies allow us to suggest candidate interfacial amino acids crucial in controlling assembly. This work deepens our understanding of how these ferritin complexes assemble and is a useful step towards production of triggerable ferritins in which these properties can be finely designed and controlled.

  • Organizational Affiliation

    Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland. soumyabiochem@gmail.com Jonathan.heddle@uj.edu.pl.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
164Thermotoga maritima MSB8Mutation(s): 1 
Gene Names: TM_1128
Find proteins for Q9X0L2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0L2 
Go to UniProtKB:  Q9X0L2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0L2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LFA

Download Ideal Coordinates CCD File 
EA [auth C],
IB [auth H],
SA [auth E],
X [auth B]
C20 H42
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
BB [auth G]
CB [auth G]
DB [auth G]
FA [auth C]
AA [auth B],
BB [auth G],
CB [auth G],
DB [auth G],
FA [auth C],
FB [auth H],
GA [auth C],
HA [auth C],
J [auth A],
JA [auth D],
JB [auth H],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
Q [auth A],
QA [auth E],
S [auth B],
T [auth B],
TA [auth E],
V [auth B],
VA [auth F],
XA [auth F],
Y [auth B],
Z [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth G]
CA [auth C]
DA [auth C]
GB [auth H]
HB [auth H]
AB [auth G],
CA [auth C],
DA [auth C],
GB [auth H],
HB [auth H],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
RA [auth E],
U [auth B],
W [auth B],
WA [auth F],
ZA [auth G]
C3 H8 O3
Query on FE

Download Ideal Coordinates CCD File 
BA [auth C]
EB [auth H]
I [auth A]
IA [auth D]
PA [auth E]
BA [auth C],
EB [auth H],
I [auth A],
IA [auth D],
PA [auth E],
R [auth B],
UA [auth F],
YA [auth G]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.219α = 90
b = 176.219β = 90
c = 355.045γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandHoming/2017-3/22

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description