9JB5 | pdb_00009jb5

Crystal structure of Arabidopsis theliana FRATAXIN HOMOLOG

• PDB DOI: https://doi.org/10.2210/pdb9JB5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-26 Released: 2025-01-01 
• Deposition Author(s): Zhang, J., Wang, J., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: in silico

Literature

Characterization of Arabidopsis thaliana FRATAXIN HOMOLOG in heme catabolism.

Zhang, J., Zhou, Y., Duan, Q., Xu, X., Wang, X., Wang, J., Liu, L.

(2025) Biochimie 231: 110-115

• PubMed: 39722354 
• DOI: https://doi.org/10.1016/j.biochi.2024.12.010
• Primary Citation of Related Structures:  
  9JB5


• PubMed Abstract: 
  

  Frataxin plays vital roles in various iron related processes. Arabidopsis thaliana FRATAXIN HOMOLOG (AtFH) is the first identified plant frataxin and has been found to regulate the last step of heme biosynthesis. Here, we report the involvement of AtFH in heme catabolism by regulating the activity of heme oxygenase. AtFH forms a homodimer, and its crystal structure shows the dimeric interactions. A structural comparison with known frataxin structures suggests the iron binding sites, and the site for heme oxygenase activity is possibly located in a region containing Glu78. The results indicate a previously uncharacterized role of plant frataxin in heme catabolism.

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Organizational Affiliation: 
• School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China.
School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China. Electronic address: [e-mail].
School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.45 kDa 
• Atom Count: 1,909 
• Modeled Residue Count: 235 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frataxin, mitochondrial	A, B	132	Arabidopsis thaliana	Mutation(s): 0  Gene Names: FH, At4g03240, F4C21.17 EC: 1.16.3.1
UniProt
Find proteins for Q9ZR07 (Arabidopsis thaliana) Explore Q9ZR07  Go to UniProtKB:  Q9ZR07

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.944	α = 90
b = 139.413	β = 90
c = 83.292	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Zhang, J., Wang, J., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32201041

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release
  
• Version 1.1: 2025-01-08
  Changes: Database references
• Version 1.2: 2025-03-19
  Changes: Database references