6FTV

X-ray structure of human heavy chain ferritin in complex with NAMI A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The NAMI A - human ferritin system: a biophysical characterization.

Ciambellotti, S.Pratesi, A.Severi, M.Ferraro, G.Alessio, E.Merlino, A.Messori, L.

(2018) Dalton Trans 47: 11429-11437

  • DOI: 10.1039/c8dt00860d

  • PubMed Abstract: 
  • The reaction of the antimetastatic ruthenium(iii) drug NAMI A with human H-chain ferritin (HuHf) was investigated through a variety of biophysical methods. We observed that the addition of HuHf to NAMI A solutions significantly increases the rate of ...

    The reaction of the antimetastatic ruthenium(iii) drug NAMI A with human H-chain ferritin (HuHf) was investigated through a variety of biophysical methods. We observed that the addition of HuHf to NAMI A solutions significantly increases the rate of spontaneous NAMI A hydrolysis suggesting the occurrence of a direct metallodrug-protein interaction. The resulting hydrolyzed Ru species binds the protein mostly forming a relatively tight 1 : 1 ruthenium/ferritin (subunit) adduct that was then separated and characterized. Notably, this adduct shows a characteristic CD spectrum in the visible region, which is diagnostic of the existence of at least one protein bound ruthenium center. The crystal structure of this NAMI A/HuHf adduct was subsequently solved at 1.58 Å resolution; clear evidence is given for the selective binding of a single Ru ion to His105 of each subunit with concomitant release of all other original Ru ligands in agreement with previous observations. We also noted that NAMI A produces a partial inhibition of HuHf ferroxidase activity. The implications of the above results are discussed.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin heavy chain
A
182Homo sapiensMutation(s): 0 
Gene Names: FTH1 (FTH, FTHL6)
EC: 1.16.3.1
Find proteins for P02794 (Homo sapiens)
Go to Gene View: FTH1
Go to UniProtKB:  P02794
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RU
Query on RU

Download SDF File 
Download CCD File 
A
RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.142 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 182.380α = 90.00
b = 182.380β = 90.00
c = 182.380γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references