5ERK | pdb_00005erk

X-ray structure of horse spleen apoferritin (control)

• PDB DOI: https://doi.org/10.2210/pdb5ERK/pdb

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


• Deposited: 2015-11-14 Released: 2016-03-02 
• Deposition Author(s): Pontillo, N., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.181 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Cisplatin encapsulation within a ferritin nanocage: a high-resolution crystallographic study.

Pontillo, N., Pane, F., Messori, L., Amoresano, A., Merlino, A.

(2016) Chem Commun (Camb) 52: 4136-4139

• PubMed: 26888424 
• DOI: https://doi.org/10.1039/c5cc10365g
• Primary Citation Related Structures: 
  5ERJ, 5ERK


• PubMed Abstract: 
  

  Cisplatin (CDDP) can be encapsulated within the central cavity of reconstituted (apo)ferritin, (A)Ft, to form a drug-loaded protein of potential great interest for targeted cancer treatments. In this study, the interactions occurring between cisplatin and native horse spleen Ft in CDDP-encapsulated AFt are investigated by high-resolution X-ray crystallography. A protein bound Pt center is unambiguously identified in AFt subunits by comparative analysis of difference Fourier electron density maps and of anomalous dispersion data. Indeed, a [Pt(NH3)2H2O](2+) fragment is found coordinated to the His132 residue located on the inner surface of the large AFt spherical cage. Remarkably, Pt binding does not alter the overall physicochemical features (shape, volume, polarity/hydrophobicity and electrostatic potential) of the outer surface of the AFt nanocage. CDDP-encapsulated AFt appears to be an ideal nanocarrier for CDDP delivery to target sites, as it possesses high biocompatibility and can be internalized by receptor mediated endocytosis, thus carrying the drug to tumor tissue with higher selectivity than free CDDP.

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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. [e-mail].
Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.
Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy. [e-mail] and 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: 21.72 kDa 
• Atom Count: 1,696 
• Modeled Residue Count: 173 
• 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
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], L [auth A], M [auth A], N [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	R [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	S [auth A], T [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.181 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.619	α = 90
b = 180.619	β = 90
c = 180.619	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Pontillo, N., Merlino, A.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations