Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation.
Abstract: We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 A and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f" = 3.6 e-) of cadmium at 1.375 A, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f" = 0.44 e-).
Publication Date: 1998-06-17 PubMed ID: 9626706 The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Comparative Study
- Journal Article
Summary
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The researchers delve into the study and refinement of the structure of a horse protein, L-chain apoferritin, and identify new cadmium binding sites believed to be associated with the process of iron loading.
Exploring Horse Protein Structure and Cadmium Binding
- The core focus of this research was to refine the structure of horse L-chain apoferritin, a specific protein in horses. The study compared its tetragonal form with the cubic form that was previously refined to a similar resolution.
- Main differences identified between the two structures pertained to cadmium ions bound to the molecule residues, specifically E130, at the threefold axes.
- With the clear signal of cadmium at a wavelength 1.375 A, anomalous Fourier difference maps were developed using the refined model phases.
Unearthing Anomalous Scatterers and New Cadmium Binding Sites
- The maps created during the study revealed the positions of anomalous scatterers, which are found in different sites within the protein structure.
- Some of these scatterers were identified near residues that were previously known to bind metal ions, including C48, E57, C126, D127, E130, and H132.
- Interestingly, new cadmium binding sites were discovered near residues E53, E56, E57, E60, and H114, which had been previously suggested to be integral to the process of iron loading.
Importance of Noncrystallographic Symmetry Map Averaging
- The researchers observed a significant increase in the quality of the anomalous Fourier difference map due to noncrystallographic symmetry map averaging.
- The refined maps helped to showcase density peaks that coincided with the positions of Met and Cys sulfur atoms, categorized as weak anomalous scatterers with an f” value of 0.44 e-. This finding adds further insight to the interactions and complexities inherent in protein structures and how different elements bind.
Cite This Article
APA
Granier T, Comberton G, Gallois B, d'Estaintot BL, Dautant A, Crichton RR, Précigoux G.
(1998).
Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation.
Proteins, 31(4), 477-485.
Publication
Researcher Affiliations
- Unité de Biophysique Structurale, CNRS, Université Bordeaux I, Talence, France. tgranier@ubs.u-bordeaux.fr
MeSH Terms
- Animals
- Apoferritins / chemistry
- Binding Sites
- Cadmium / metabolism
- Crystallography, X-Ray
- Ferritins / metabolism
- Fourier Analysis
- Horses
- Models, Molecular
- Protein Binding
- Scattering, Radiation
Citations
This article has been cited 5 times.- Viviani VR, Pelentir GF, Bevilaqua VR. Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing. Biosensors (Basel) 2022 Jun 10;12(6).
- Pozzi C, Ciambellotti S, Bernacchioni C, Di Pisa F, Mangani S, Turano P. Chemistry at the protein-mineral interface in L-ferritin assists the assembly of a functional (μ(3)-oxo)Tris[(μ(2)-peroxo)] triiron(III) cluster. Proc Natl Acad Sci U S A 2017 Mar 7;114(10):2580-2585.
- Kumar A, Glembo TJ, Ozkan SB. The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin. Biophys J 2015 Sep 15;109(6):1273-81.
- Masuda T, Goto F, Yoshihara T, Mikami B. Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin. J Biol Chem 2010 Feb 5;285(6):4049-4059.
- Bradley JM, Bugg Z, Moore GR, Hemmings AM, Le Brun NE. Observation of the Assembly of the Nascent Mineral Core at the Nucleation Site of Human Mitochondrial Ferritin. J Am Chem Soc 2025 Apr 23;147(16):13699-13710.
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