9KF8 | pdb_00009kf8

Crystal structure of ferritin mutant (E53H/E57H/E60H/R64H)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.171 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.170 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An Artificial Metal-Free Peroxidase Designed Using a Ferritin Cage for Bioinspired Catalysis.

Tian, J.Maity, B.Furuta, T.Pan, T.Ueno, T.

(2025) Angew Chem Int Ed Engl 64

  • DOI: https://doi.org/10.1002/anie.202504608
  • Primary Citation of Related Structures:  
    9KF5, 9KF7, 9KF8, 9KF9, 9KFA

  • PubMed Abstract: 

    Developing artificial enzymes is challenging because it requires precise design of active sites with well-arranged amino acid residues. Histidine-rich oligopeptides have been recently shown to exhibit peroxidase-mimetic activities, but their catalytic function relies on maintaining unique supramolecular structures. This work demonstrates the design of a specific array of histidine residues on the internal surface of the ferritin cage to function as an active center for catalysis. The crystal structures of the ferritin mutants revealed histidine-histidine interactions, forming well-defined histidine clusters (His-clusters). These mutants exhibit peroxidase-mimetic activities by oxidizing 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide. Molecular dynamics simulations further highlight the co-localization of TMB and hydrogen peroxide at the histidine-rich clusters, indicating that the confined environment of the ferritin cage enhances their interactions. This study presents a simple yet effective approach to design metal-free artificial enzymes, paving the way for innovations in bioinspired catalysis.


  • Organizational Affiliation
    • School of Life Science and Technology, Institute of Science Tokyo, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chain174Equus caballusMutation(s): 4 
Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
T [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.171 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.170 (DCC) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.93α = 90
b = 180.93β = 90
c = 180.93γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references