6TSX

Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 30 minutes

• PDB DOI: https://doi.org/10.2210/pdb6TSX/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2019-12-21 Released: 2020-02-19 
• Deposition Author(s): Pozzi, C., Ciambellotti, S., Turano, P., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.221 
• R-Value Work: 0.184 

Literature

Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin.

Ciambellotti, S., Pozzi, C., Mangani, S., Turano, P.

(2020) Chemistry 26: 5770-5773

• PubMed: 32027764 
• DOI: https://doi.org/10.1002/chem.202000064
• Primary Citation of Related Structures:  
  6TR9, 6TRZ, 6TS0, 6TS1, 6TSA, 6TSF, 6TSJ, 6TSS, 6TSX


• PubMed Abstract: 
  

  X-ray structures of homopolymeric human L-ferritin and horse spleen ferritin were solved by freezing protein crystals at different time intervals after exposure to a ferric salt and revealed the growth of an octa-nuclear iron cluster on the inner surface of the protein cage with a key role played by some glutamate residues. An atomic resolution view of how the cluster formation develops starting from a (μ ³ -oxo)tris[(μ ² -glutamato-κO:κO')](glutamato-κO)(diaquo)triiron(III) seed is provided. The results support the idea that iron biomineralization in ferritin is a process initiating at the level of the protein surface, capable of contributing coordination bonds and electrostatic guidance.

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Organizational Affiliation: 

Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, 50019, Italy.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 21.13 kDa 
• Atom Count: 1,476 
• Modelled Residue Count: 169 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A [auth AAA]	175	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	P [auth AAA]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], Q [auth AAA], R [auth AAA], S [auth AAA], T [auth AAA], U [auth AAA]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	V [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
O	B [auth AAA], C [auth AAA], D [auth AAA], E [auth AAA]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A [auth AAA]	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.221 
• R-Value Work: 0.184 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.242	α = 90
b = 181.242	β = 90
c = 181.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Pozzi, C., Ciambellotti, S., Turano, P., Mangani, S.

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-05-20
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description