3AJO

Crystal structure of wild-type human ferritin H chain

• PDB DOI: https://doi.org/10.2210/pdb3AJO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-11 Released: 2010-08-25 
• Deposition Author(s): Masuda, T., Mikami, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.183 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

The universal mechanism for iron translocation to the ferroxidase site in ferritin, which is mediated by the well conserved transit site

Masuda, T., Goto, F., Yoshihara, T., Mikami, B.

(2010) Biochem Biophys Res Commun 400: 94-99

• PubMed: 20705053 
• DOI: https://doi.org/10.1016/j.bbrc.2010.08.017
• Primary Citation of Related Structures:  
  3AJO, 3AJP, 3AJQ


• PubMed Abstract: 
  

  Ferritins are ubiquitous iron storage proteins. Recently, we identified a novel metal-binding site, transit site, in the crystal structure of phytoferritin. To elucidate the function of the transit site in ferritin from other species, we prepared transit-site-deficient mutants of human H ferritin, E140A and E140Q, and their iron oxidation kinetics was analyzed. The initial velocities of iron oxidization were reduced in the variants, especially in E140Q. The crystal structure of E140Q showed that the side chain of the mutated Gln140 was fixed by a hydrogen bond, whereas that of native Glu140 was flexible. These results suggest that the conserved transit site also has a function to assist with the metal ion sequestration to the ferroxidase site in ferritins from vertebrates.

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Organizational Affiliation: 

Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 21.42 kDa 
• Atom Count: 1,714 
• Modelled Residue Count: 172 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	A	182	Homo sapiens	Mutation(s): 0  Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens) Explore P02794  Go to UniProtKB:  P02794
PHAROS:  P02794 GTEx:  ENSG00000167996

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A], D [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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.183 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.723	α = 90
b = 182.723	β = 90
c = 182.723	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Masuda, T., Mikami, B.

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description