6HJT | pdb_00006hjt

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 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

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 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.
EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom.
Institute of Pharmaceutical Science, King's College London, Stamford Street, London SE1 9NH, United Kingdom.

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 
• Modeled 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 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

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