5MIJ | pdb_00005mij

X-ray structure of carboplatin-encapsulated horse spleen apoferritin

• PDB DOI: https://doi.org/10.2210/pdb5MIJ/pdb

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


• Deposited: 2016-11-28 Released: 2017-03-15 
• Deposition Author(s): Pontillo, N., Ferraro, G., Helliwell, J.R., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.181 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

X-ray Structure of the Carboplatin-Loaded Apo-Ferritin Nanocage.

Pontillo, N., Ferraro, G., Helliwell, J.R., Amoresano, A., Merlino, A.

(2017) ACS Med Chem Lett 8: 433-437

• PubMed: 28435532 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00025
• Primary Citation Related Structures: 
  5MIJ, 5MIK


• PubMed Abstract: 
  

  The second-generation Pt anticancer agent carboplatin (CBDCA) was encapsulated within the apo horse spleen ferritin (AFt) nanocage, and the X-ray structure of the drug-loaded protein was refined at 1.49 Å resolution. Two Pt binding sites, different from the one observed in the cisplatin-encapsulated AFt, were identified in Ft subunits by inspection of anomalous electron density maps at two wavelengths and difference Fourier electron density maps, which provide the necessary sensitivity to discriminate between Pt from CBDCA and Cd ions that are present in the crystallization conditions. Pt centers coordinate to the NE2 atom of His49 and to the NE2 atom of His132, both on the inner surface of the Ft nanocage.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Napoli, Italy.
School of Chemistry, Faculty of Engineering and Physical Sciences, University of Manchester, Brunswick Street, Manchester M13 9PL, England.
CNR Institute of Biostructures and Bioimages, Via Mezzocannone 16, I-80126 Napoli, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.74 kDa 
• Atom Count: 1,782 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	Q [auth A], R [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], I [auth A], J [auth A], K [auth A], O [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	P [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	L [auth A], M [auth A], N [auth A], S [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.181 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.67	α = 90
b = 181.67	β = 90
c = 181.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Pontillo, N., Ferraro, G., Helliwell, J.R., Merlino, A.

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations