{
  "abstract": "Microbial rhodopsins are photoreceptors with a conserved seven-transmembrane core architecture that use the chromophore retinal-a vitamin A derivative-to convert light absorption into ion transport, signaling, and enzymatic activity. Since their discovery half a century ago, genome sequencing has uncovered thousands of these proteins across archaea, bacteria, eukaryotes, and viruses, revealing a diverse functional repertoire that includes ion pumps and channels, transducer activators, and enzyme/channel regulators. Although the structure of the seven-transmembrane bundle core and the retinal-binding pocket is highly conserved, the sequence identity across major classes is low. This low sequence identity, combined with the rapidly expanding number of microbial rhodopsins identified by metagenomics, makes direct comparisons across the superfamily increasingly difficult. Here, we introduce a generic residue-numbering system for microbial rhodopsins (MO numbering system), a structure-guided framework anchored to the retinal-binding pocket that enables consistent residue comparison across even the most divergent family members. Analyzing 129 structures and approximately 40,000 sequences, we demonstrate its utility by analyzing sequence-structure-function relationships across the superfamily, including previously uncharacterized members. The MO numbering system provides a common language for organizing the growing repertoire of microbial rhodopsins, integrating structural, spectroscopic, and electrophysiological data, and engineering next-generation optogenetic tools.",
  "abstract_shown": true,
  "affiliations": [
    "Condensed Matter Theory Group, PSI Center for Scientific Computing, Theory and Data, Villigen-PSI, Switzerland.",
    "Department of Biology, ETH Zürich, Zürich, Switzerland.",
    "Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.",
    "Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo Japan.",
    "Department of Life Sciences, School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo Japan.",
    "Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.",
    "Institute for Extra-cutting-edge Science and Technology Avant-garde Research of Life (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan.",
    "Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.",
    "Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.",
    "Laboratory of Biomolecular Research, PSI Center for Life Sciences, Villigen-PSI, Switzerland.",
    "Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo Japan.",
    "FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama Japan.",
    "CREST, Japan Science and Technology Agency, Kawaguchi, Saitama Japan."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Flurin S Hidber"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Seiya Tajima"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Koichiro E Kishi"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Yosuke Nishimura"
    },
    {
      "affs": [
        5,
        7,
        8
      ],
      "name": "Susumu Yoshizawa"
    },
    {
      "affs": [
        0,
        2,
        9
      ],
      "name": "Xavier Deupi"
    },
    {
      "affs": [
        3,
        4,
        10,
        11,
        12
      ],
      "name": "Hideaki E Kato"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6x9s3r1aq909e.bib",
  "cited_by": 0,
  "doi": "10.1038/s44511-026-00004-w",
  "fulltext_url": "https://europepmc.org/articles/PMC13739731",
  "id": "6x9s3r1aq909e",
  "issns": [
    "3091-3888"
  ],
  "landing_url": "https://europepmc.org/article/MED/42996294",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2804|Photoreceptor and optogenetics research"
    ]
  ],
  "openalex": "W7225317018",
  "pdf_url": "https://europepmc.org/articles/PMC13739731?pdf=render",
  "pmcid": "PMC13739731",
  "pmid": "42996294",
  "published": "2026-11-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6x9s3r1aq909e.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T15:20:34Z",
      "native_id": "MED:42996294",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42996294"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:2804|Photoreceptor and optogenetics research",
      "subfield": "neuroscience"
    }
  ],
  "title": "A generic residue-numbering system for microbial rhodopsins.",
  "title_text": "A generic residue-numbering system for microbial rhodopsins.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T15:20:34Z",
  "url": "https://research.draconitic.com/paper/6x9s3r1aq909e",
  "venue": "Npj structural biology",
  "versions": []
}