1BG7 | pdb_00001bg7

LOCALIZED UNFOLDING AT THE JUNCTION OF THREE FERRITIN SUBUNITS. A MECHANISM FOR IRON RELEASE?

• PDB DOI: https://doi.org/10.2210/pdb1BG7/pdb

• Classification: IRON STORAGE
• Organism(s): Aquarana catesbeiana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1998-06-05 Released: 1999-01-13 
• Deposition Author(s): Takagi, H., Shi, D., Ha, Y., Allewell, N.M., Theil, E.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Localized unfolding at the junction of three ferritin subunits. A mechanism for iron release?

Takagi, H., Shi, D., Ha, Y., Allewell, N.M., Theil, E.C.

(1998) J Biological Chem 273: 18685-18688

• PubMed: 9668036 
• DOI: https://doi.org/10.1074/jbc.273.30.18685
• Primary Citation Related Structures: 
  1BG7


• PubMed Abstract: 
  

  How and where iron exits from ferritin for cellular use is unknown. Twenty-four protein subunits create a cavity in ferritin where iron is concentrated >10(11)-fold as a mineral. Proline substitution for conserved leucine 134 (L134P) allowed normal assembly but increased iron exit rates. X-ray crystallography of H-L134P ferritin revealed localized unfolding at the 3-fold axis, also iron entry sites, consistent with shared use sites for iron exit and entry. The junction of three ferritin subunits appears to be a dynamic aperture with a "shutter" that cytoplasmic factors might open or close to regulate iron release in vivo.

---

Organizational Affiliation: 
• Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 20.59 kDa 
• Atom Count: 1,267 
• Modeled Residue Count: 153 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERRITIN	A	176	Aquarana catesbeiana	Mutation(s): 2  EC: 1.16.3.1
UniProt
Find proteins for P07229 (Aquarana catesbeiana) Explore P07229  Go to UniProtKB:  P07229

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.8	α = 90
b = 182.8	β = 90
c = 182.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Takagi, H., Shi, D., Ha, Y., Allewell, N.M., Theil, E.C.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations, Other
• Version 1.5: 2023-08-02
  Changes: Refinement description
• Version 1.6: 2024-05-22
  Changes: Data collection