Evidence map›Paper›PMID 34728609›Full record

ArticleNature communications2021

A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex.

Kazutoshi Tani, Kenji V P Nagashima, Ryo Kanno, Saki Kawamura, Riku Kikuchi, Malgorzata Hall, Long-Jiang Yu, Yukihiro Kimura, Michael T Madigan, Akira Mizoguchi and 2 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
2.4field-weighted citation impact, top 10% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 41 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 7 institutions in 3 countries.

Kazutoshi TaniGraduate School of Medicine, Mie University, Tsu, 514-8507, Japan. ktani@doc.medic.mie-u.ac.jp.ORCID 0000-0003-4835-154X
Kenji V P NagashimaResearch Institute for Integrated Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan.
Ryo KannoImaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
Saki KawamuraFaculty of Science, Ibaraki University, Mito, 310-8512, Japan.
Riku KikuchiFaculty of Science, Ibaraki University, Mito, 310-8512, Japan.
Malgorzata HallImaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
Long-Jiang YuPhotosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.ORCID 0000-0002-4962-1049
Yukihiro KimuraDepartment of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan.ORCID 0000-0003-3747-0367
Michael T MadiganSchool of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA.
Akira MizoguchiGraduate School of Medicine, Mie University, Tsu, 514-8507, Japan.
Bruno M HumbelImaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
Zheng-Yu Wang-OtomoFaculty of Science, Ibaraki University, Mito, 310-8512, Japan. wang@ml.ibaraki.ac.jp.ORCID 0000-0003-1676-2002
Ibaraki University · JPOkinawa Institute of Science and Technology Graduate University · JPMie University · JPChinese Academy of Sciences · CNKanagawa University · JPKobe University · JPSouthern Illinois University Carbondale · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.

Indexed as

Bacterial ProteinsCryoelectron MicroscopyDimerizationLight-Harvesting Protein ComplexesMembrane ProteinsModels, MolecularPhotosynthetic Reaction Center Complex ProteinsProtein ConformationRhodobacter sphaeroidesBacterial ProteinsLight-Harvesting Protein ComplexesMembrane ProteinsPhotosynthetic Reaction Center Complex Proteins

Identifiers

PMID34728609
PMCPMC8564508
OpenAlexW3209543651

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.