Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides

Tani, Kazuhide; Kanno, Ryo; Makino, Yuki; Hall, Malgorzata; Takenouchi, Mizuki; Imanishi, Masaaki; Yu, Long-Jiang; Overmann, Jörg; Madigan, Michael T.; Kimura, Yukihiro; Mizoguchi, Akira; Humbel, Bruno M.; Wang-Otomo, Zheng-Yu

doi:10.1038/s41467-020-18748-3

Cited by 42 publications

(87 citation statements)

References 54 publications

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“…Most CL molecules were located on the cytoplasmic side of the membrane with their head groups pointing toward the membrane surface, whereas most PG and PE molecules were distributed on the periplasmic side. This phospholipid distribution is similar to that observed in other LH1-RCs 3,6,11,12 . Channels were found between every adjacent pair of LH1 αβ-polypeptides (Fig.…”

supporting

confidence: 88%

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Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

Tani

Kanno

et al. 2021

Preprint

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We present a cryo-EM structure of the light-harvesting-reaction center (LH1-RC) core complex from purple phototrophic bacterium Rhodospirillum (Rsp.) rubrum at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected rhodoquinone (RQ) molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol sidechains of bacteriochlorophyll (BChl) aG coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls aG. The structure also revealed key protein–protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our findings enable to evaluate past experimental and computational results obtained with this widely used organism and provide crucial information for more detailed exploration of light-energy conversion, quinone transport, and structure—function relationships in pigment-protein complexes.

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supporting

confidence: 88%

“…S4). Similar channels have also been observed in other LH1 complexes with closed ring-like structures 3,6,12 , suggesting that these hydrophobic channels function as paths for quinone transport into and out of the complex. Such a function is supported by molecular dynamics simulation 13 and biochemical analysis 14 .…”

supporting

confidence: 76%

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

Tani

Kanno

et al. 2021

Preprint

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“…strain 970 RC-LH1s (fig. S12, B to E) ( 9 , 12 ), and hydrogen-bonding residues to the lipid head groups appear reasonably well conserved in sequence alignments (fig. S13), indicating that, in addition to a conserved CDL bound to the RC ( 24 ), these sites may be conserved in RC-LH1 complexes.…”

Section: Resultsmentioning

confidence: 83%

“…tepidum [Protein Data Bank (PDB) ID 5Y5S] ( 9 ), Thiorhodovibrio ( Trv. ) strain 970 (PDB ID 7C9R) ( 12 ), and Blastochloris ( Blc. ) viridis (PDB ID 6ET5) ( 10 ).…”

Section: Resultsmentioning

confidence: 99%

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Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels

et al. 2021

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The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo–electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris. A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC QB site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.

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Tunneling Mechanisms of Quinones in Photosynthetic Reaction Center–Light Harvesting 1 Supercomplexes

Mao,

Guo,

Bie

et al. 2024

Small Science

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In photosynthesis, light energy is absorbed and transferred to the reaction center, ultimately leading to the reduction of quinone molecules through the electron transfer chain. The oxidation and reduction of quinones generate an electrochemical potential difference used for adenosine triphosphate synthesis. The trafficking of quinone/quinol molecules between electron transport components has been a long‐standing question. Here, an atomic‐level investigation into the molecular mechanism of quinol dissociation in the photosynthetic reaction center–light‐harvesting complex 1 (RC–LH1) supercomplexes from Rhodopseudomonas palustris, using classical molecular dynamics (MD) simulations combined with self‐random acceleration MD‐MD simulations and umbrella sampling methods, is conducted. Results reveal a significant increase in the mobility of quinone molecules upon reduction within RC–LH1, which is accompanied by conformational modifications in the local protein environment. Quinol molecules have a tendency to escape from RC–LH1 in a tail‐first mode, exhibiting channel selectivity, with distinct preferred dissociation pathways in the closed and open LH1 rings. Furthermore, comparative analysis of free energy profiles indicates that alternations in the protein environment accelerate the dissociation of quinol molecules through the open LH1 ring. In particular, aromatic amino acids form π‐stacking interactions with the quinol headgroup, resembling the key components in a conveyor belt system. This study provides insights into the molecular mechanisms that govern quinone/quinol exchange in bacterial photosynthesis and lays the framework for tuning electron flow and energy conversion to improve metabolic performance.

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Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides

Cited by 42 publications

References 54 publications

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels

Tunneling Mechanisms of Quinones in Photosynthetic Reaction Center–Light Harvesting 1 Supercomplexes

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