Letter | Published:

Charge-density analysis of an iron–sulfur protein at an ultra-high resolution of 0.48 Å

Nature volume 534, pages 281284 (09 June 2016) | Download Citation

Abstract

The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0–1.5 Å resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints1,2. Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with pre-existing common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins3. Here we report a charge-density analysis of the high-potential iron–sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 Å. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3d and sulfur 3p electron densities of the Fe4S4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron–sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.

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Protein Data Bank

Data deposits

The coordinates and structure factors have been deposited in the Protein Data Bank under accession number 5D8V.

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Acknowledgements

We thank K. Kusumoto and H. Ohno for their contributions in the initial steps of the work, and T. Tsujinaka and S. Niwa for their contributions in the preparation of the manuscript. We also thank the BL41XU beamline staff of SPring-8 for their help in data collection. This work was supported by a Grant-in-Aid for Scientific Research (number 23657073 to K.T.) and the Photon and Quantum Basic Research Coordinated Development Program (to K.M.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

Author information

Author notes

    • Yu Hirano
    •  & Kazuki Takeda

    These authors contributed equally to this work.

    • Yu Hirano

    Present address: Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai-mura, Ibaraki 319-1195, Japan.

Affiliations

  1. Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan

    • Yu Hirano
    • , Kazuki Takeda
    •  & Kunio Miki

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Contributions

K.M. initiated and supervised the project. K.T. designed the experiments. Y.H. prepared crystals. Y.H. and K.T. performed data collection and the crystallographic analysis. Y.H., K.T. and K.M. discussed the results. Y.H. wrote the initial draft, and K.T. and K.M. revised the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Kunio Miki.

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https://doi.org/10.1038/nature18001

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