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Rhodobacter capsulatus forms a compact crescent-shaped LH1–RC photocomplex

Author

Listed:
  • Kazutoshi Tani

    (Mie University)

  • Ryo Kanno

    (Okinawa Institute of Science and Technology Graduate University (OIST)
    Okinawa Institute of Science and Technology Graduate University (OIST))

  • Xuan-Cheng Ji

    (Ibaraki University)

  • Itsusei Satoh

    (Ibaraki University)

  • Yuki Kobayashi

    (Ibaraki University)

  • Malgorzata Hall

    (Okinawa Institute of Science and Technology Graduate University (OIST))

  • Long-Jiang Yu

    (Chinese Academy of Sciences)

  • Yukihiro Kimura

    (Kobe University)

  • Akira Mizoguchi

    (Mie University)

  • Bruno M. Humbel

    (Okinawa Institute of Science and Technology Graduate University (OIST)
    Juntendo University, Graduate School of Medicine)

  • Michael T. Madigan

    (Southern Illinois University)

  • Zheng-Yu Wang-Otomo

    (Ibaraki University)

Abstract

Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the light-harvesting 1–reaction center (LH1–RC) complex, but lacks protein-U, a U-shaped polypeptide in the LH1–RC of its close relative Rba. sphaeroides. Here we present a cryo-EM structure of the Rba. capsulatus LH1–RC purified by DEAE chromatography. The crescent-shaped LH1–RC exhibits a compact structure containing only 10 LH1 αβ-subunits. Four αβ-subunits corresponding to those adjacent to protein-U in Rba. sphaeroides were absent. PufX in Rba. capsulatus exhibits a unique conformation in its N-terminus that self-associates with amino acids in its own transmembrane domain and interacts with nearby polypeptides, preventing it from interacting with proteins in other complexes and forming dimeric structures. These features are discussed in relation to the minimal requirements for the formation of LH1–RC monomers and dimers, the spectroscopic behavior of both the LH1 and RC, and the bioenergetics of energy transfer from LH1 to the RC.

Suggested Citation

  • Kazutoshi Tani & Ryo Kanno & Xuan-Cheng Ji & Itsusei Satoh & Yuki Kobayashi & Malgorzata Hall & Long-Jiang Yu & Yukihiro Kimura & Akira Mizoguchi & Bruno M. Humbel & Michael T. Madigan & Zheng-Yu Wang, 2023. "Rhodobacter capsulatus forms a compact crescent-shaped LH1–RC photocomplex," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36460-w
    DOI: 10.1038/s41467-023-36460-w
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    References listed on IDEAS

    as
    1. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
    2. Patrick Bryant & Gabriele Pozzati & Arne Elofsson, 2022. "Improved prediction of protein-protein interactions using AlphaFold2," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
    4. Patrick Bryant & Gabriele Pozzati & Arne Elofsson, 2022. "Author Correction: Improved prediction of protein-protein interactions using AlphaFold2," Nature Communications, Nature, vol. 13(1), pages 1-1, December.
    5. Kazutoshi Tani & Kenji V. P. Nagashima & Ryo Kanno & Saki Kawamura & Riku Kikuchi & Malgorzata Hall & Long-Jiang Yu & Yukihiro Kimura & Michael T. Madigan & Akira Mizoguchi & Bruno M. Humbel & Zheng-Y, 2021. "A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    6. Ewen Callaway, 2023. "After AlphaFold: protein-folding contest seeks next big breakthrough," Nature, Nature, vol. 613(7942), pages 13-14, January.
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