6HJT

The X-ray structure of the horse spleen ferritin nanocage containing Pt, obtained upon encapsulation of a Pt(II) terpyridine compound within the protein cage

• PDB DOI: https://doi.org/10.2210/pdb6HJT/pdb

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


• Deposited: 2018-09-04 Released: 2018-12-19 
• Deposition Author(s): Pica, A., Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.157 
• R-Value Work: 0.127 
• R-Value Observed: 0.129 

Literature

Preparation, structure, cytotoxicity and mechanism of action of ferritin-Pt(II) terpyridine compound nanocomposites.

Ferraro, G., Pica, A., Petruk, G., Pane, F., Amoresano, A., Cilibrizzi, A., Vilar, R., Monti, D.M., Merlino, A.

(2018) Nanomedicine (Lond) 13: 2995-3007

• PubMed: 30501559 
• DOI: https://doi.org/10.2217/nnm-2018-0259
• Primary Citation of Related Structures:  
  6HJT, 6HJU


• PubMed Abstract: 
  

  A Pt(II)-terpyridine compound, bearing two piperidine substituents at positions 2 and 2' of the terpyridine ligand (1), is highly cytotoxic and shows a mechanism of action distinct from cisplatin. 1 has been incorporated within the ferritin nanocage (AFt). Spectroscopic and crystallographic data of the Pt(II)-AFt nanocomposite have been collected and in vitro anticancer activity has been explored using cancer cells. Pt(II)-containing fragments bind His49, His114 and His132. Pt(II)-AFt nanocomposite is less cytotoxic than 1, but it is more toxic than cisplatin at high concentrations. The Pt(II)-AFt nanocomposite triggers necrosis in cancer cells, as free 1 does. Pt(II)-AFt nanocomposites are promising vehicles to deliver Pt-based drugs to cancer cells.

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Organizational Affiliation: 

Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 22.01 kDa 
• Atom Count: 1,889 
• Modelled Residue Count: 172 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A	174	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	P [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	R [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	I [auth A], J [auth A], S [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.157 
• R-Value Work: 0.127 
• R-Value Observed: 0.129 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.156	α = 90
b = 181.156	β = 90
c = 181.156	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Pica, A., Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Derived calculations