Crystal structure of the red light-activated channelrhodopsin Chrimson View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Kazumasa Oda, Johannes Vierock, Satomi Oishi, Silvia Rodriguez-Rozada, Reiya Taniguchi, Keitaro Yamashita, J. Simon Wiegert, Tomohiro Nishizawa, Peter Hegemann, Osamu Nureki

ABSTRACT

Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissues and also enables dual-color experiments in combination with blue-light-activated optogenetic tools. Here we report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama, Chrimson, at 2.6 Å resolution. Chrimson resembles prokaryotic proton pumps in the retinal binding pocket, while sharing similarity with other channelrhodopsins in the ion-conducting pore. Concomitant mutation analysis identified the structural features that are responsible for Chrimson's red light sensitivity; namely, the protonation of the counterion for the retinal Schiff base, and the polar residue distribution and rigidity of the retinal binding pocket. Based on these mechanistic insights, we engineered ChrimsonSA, a mutant with a maximum activation wavelength red-shifted beyond 605 nm and accelerated closing kinetics. More... »

PAGES

3949

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41467-018-06421-9

DOI

http://dx.doi.org/10.1038/s41467-018-06421-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1107129366

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30258177


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0299", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Other Physical Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/02", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Physical Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Oda", 
        "givenName": "Kazumasa", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Humboldt University of Berlin", 
          "id": "https://www.grid.ac/institutes/grid.7468.d", 
          "name": [
            "Institute of Biology, Experimental Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115, Berlin, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vierock", 
        "givenName": "Johannes", 
        "id": "sg:person.01103001460.23", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01103001460.23"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Oishi", 
        "givenName": "Satomi", 
        "id": "sg:person.0752316056.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0752316056.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), 20251, Hamburg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rodriguez-Rozada", 
        "givenName": "Silvia", 
        "id": "sg:person.013712103677.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013712103677.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Taniguchi", 
        "givenName": "Reiya", 
        "id": "sg:person.0677124351.35", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0677124351.35"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "RIKEN SPring-8 Center, 679-5198, Sayo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yamashita", 
        "givenName": "Keitaro", 
        "id": "sg:person.0624540116.94", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0624540116.94"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), 20251, Hamburg, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Wiegert", 
        "givenName": "J. Simon", 
        "id": "sg:person.0740613472.98", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0740613472.98"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Japan Science and Technology Agency", 
          "id": "https://www.grid.ac/institutes/grid.419082.6", 
          "name": [
            "Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan", 
            "Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 332-0012, Kawaguchi, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nishizawa", 
        "givenName": "Tomohiro", 
        "id": "sg:person.01033506435.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01033506435.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Humboldt University of Berlin", 
          "id": "https://www.grid.ac/institutes/grid.7468.d", 
          "name": [
            "Institute of Biology, Experimental Biophysics, Humboldt-Universit\u00e4t zu Berlin, 10115, Berlin, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hegemann", 
        "givenName": "Peter", 
        "id": "sg:person.0660723716.59", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0660723716.59"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nureki", 
        "givenName": "Osamu", 
        "id": "sg:person.01043223704.15", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043223704.15"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1107/s0907444910007493", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000235100"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444910007493", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000235100"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1936192100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001065397"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0119558", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001185730"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbabio.2013.10.014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005868184"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2014.11.004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006355659"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi901634p", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008609531"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi901634p", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008609531"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/prot.20744", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009285243"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/prot.20744", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009285243"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bpj.2014.03.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010378023"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m111.326207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013231754"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/srep14807", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015762844", 
          "https://doi.org/10.1038/srep14807"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1472-6807-8-49", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017381549", 
          "https://doi.org/10.1186/1472-6807-8-49"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms8177", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017651708", 
          "https://doi.org/10.1038/ncomms8177"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/jcc.21663", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017943993"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909052925", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020777046"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909052925", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020777046"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbabio.2013.09.006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024378839"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10870", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025722569", 
          "https://doi.org/10.1038/nature10870"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1523341113", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025957146"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nn.2247", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028782300", 
          "https://doi.org/10.1038/nn.2247"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0006-3495(94)80587-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030370402"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10360", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030639357", 
          "https://doi.org/10.1038/nature10360"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.2836", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030668007", 
          "https://doi.org/10.1038/nmeth.2836"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909047337", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032162623"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444909047337", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032162623"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00239-003-2557-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033133304", 
          "https://doi.org/10.1007/s00239-003-2557-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s0907444904023510", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033689976"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nn.3502", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037754750", 
          "https://doi.org/10.1038/nn.3502"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbagen.2014.05.021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041093715"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nn.2120", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042891337", 
          "https://doi.org/10.1038/nn.2120"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nn1525", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043162871", 
          "https://doi.org/10.1038/nn1525"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nn1525", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043162871", 
          "https://doi.org/10.1038/nn1525"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nn1525", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043162871", 
          "https://doi.org/10.1038/nn1525"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1249375", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044788697"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1072068", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047484856"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b815762f", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047567618"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1751-1097.2011.01027.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049770281"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1252367", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049887715"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06977", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051651970", 
          "https://doi.org/10.1038/nature06977"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m112.391185", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051835585"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aah3497", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051924025"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082780994", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/pdb.prot094888", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083403746"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/pdb.prot094904", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083403748"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/php.12741", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085403101"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3791/55497", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1085625508"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41598-017-09600-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091344499", 
          "https://doi.org/10.1038/s41598-017-09600-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41598-017-09600-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091344499", 
          "https://doi.org/10.1038/s41598-017-09600-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41598-017-09600-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091344499", 
          "https://doi.org/10.1038/s41598-017-09600-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aan5544", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091782644"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aan8862", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1092934582"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1107/s2059798318004576", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1103628910"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41467-018-04146-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1103640980", 
          "https://doi.org/10.1038/s41467-018-04146-3"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2018-12", 
    "datePublishedReg": "2018-12-01", 
    "description": "Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissues and also enables dual-color experiments in combination with blue-light-activated optogenetic tools. Here we report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama, Chrimson, at 2.6\u2009\u00c5 resolution. Chrimson resembles prokaryotic proton pumps in the retinal binding pocket, while sharing similarity with other channelrhodopsins in the ion-conducting pore. Concomitant mutation analysis identified the structural features that are responsible for Chrimson's red light sensitivity; namely, the protonation of the counterion for the retinal Schiff base, and the polar residue distribution and rigidity of the retinal binding pocket. Based on these mechanistic insights, we engineered ChrimsonSA, a mutant with a maximum activation wavelength red-shifted beyond 605\u2009nm and accelerated closing kinetics.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/s41467-018-06421-9", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.6822921", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6534916", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6504146", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6825069", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1043282", 
        "issn": [
          "2041-1723"
        ], 
        "name": "Nature Communications", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "Crystal structure of the red light-activated channelrhodopsin Chrimson", 
    "pagination": "3949", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "c0bd25dff50e7b1080c8ee67af21dfb8849b3902202ca05d154a0a0a5b907823"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30258177"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101528555"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41467-018-06421-9"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1107129366"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41467-018-06421-9", 
      "https://app.dimensions.ai/details/publication/pub.1107129366"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T17:37", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8672_00000548.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/s41467-018-06421-9"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-06421-9'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-06421-9'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-06421-9'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-018-06421-9'


 

This table displays all metadata directly associated to this object as RDF triples.

302 TRIPLES      21 PREDICATES      75 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41467-018-06421-9 schema:about anzsrc-for:02
2 anzsrc-for:0299
3 schema:author N747acd001dad4f96bee72b9a090141dd
4 schema:citation sg:pub.10.1007/s00239-003-2557-8
5 sg:pub.10.1038/nature06977
6 sg:pub.10.1038/nature10360
7 sg:pub.10.1038/nature10870
8 sg:pub.10.1038/ncomms8177
9 sg:pub.10.1038/nmeth.2836
10 sg:pub.10.1038/nn.2120
11 sg:pub.10.1038/nn.2247
12 sg:pub.10.1038/nn.3502
13 sg:pub.10.1038/nn1525
14 sg:pub.10.1038/s41467-018-04146-3
15 sg:pub.10.1038/s41598-017-09600-8
16 sg:pub.10.1038/srep14807
17 sg:pub.10.1186/1472-6807-8-49
18 https://app.dimensions.ai/details/publication/pub.1082780994
19 https://doi.org/10.1002/jcc.21663
20 https://doi.org/10.1002/prot.20744
21 https://doi.org/10.1016/j.bbabio.2013.09.006
22 https://doi.org/10.1016/j.bbabio.2013.10.014
23 https://doi.org/10.1016/j.bbagen.2014.05.021
24 https://doi.org/10.1016/j.bpj.2014.03.002
25 https://doi.org/10.1016/j.jmb.2014.11.004
26 https://doi.org/10.1016/s0006-3495(94)80587-9
27 https://doi.org/10.1021/bi901634p
28 https://doi.org/10.1039/b815762f
29 https://doi.org/10.1073/pnas.1523341113
30 https://doi.org/10.1073/pnas.1936192100
31 https://doi.org/10.1074/jbc.m111.326207
32 https://doi.org/10.1074/jbc.m112.391185
33 https://doi.org/10.1101/pdb.prot094888
34 https://doi.org/10.1101/pdb.prot094904
35 https://doi.org/10.1107/s0907444904023510
36 https://doi.org/10.1107/s0907444909047337
37 https://doi.org/10.1107/s0907444909052925
38 https://doi.org/10.1107/s0907444910007493
39 https://doi.org/10.1107/s2059798318004576
40 https://doi.org/10.1111/j.1751-1097.2011.01027.x
41 https://doi.org/10.1111/php.12741
42 https://doi.org/10.1126/science.1072068
43 https://doi.org/10.1126/science.1249375
44 https://doi.org/10.1126/science.1252367
45 https://doi.org/10.1126/science.aah3497
46 https://doi.org/10.1126/science.aan5544
47 https://doi.org/10.1126/science.aan8862
48 https://doi.org/10.1371/journal.pone.0119558
49 https://doi.org/10.3791/55497
50 schema:datePublished 2018-12
51 schema:datePublishedReg 2018-12-01
52 schema:description Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissues and also enables dual-color experiments in combination with blue-light-activated optogenetic tools. Here we report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama, Chrimson, at 2.6 Å resolution. Chrimson resembles prokaryotic proton pumps in the retinal binding pocket, while sharing similarity with other channelrhodopsins in the ion-conducting pore. Concomitant mutation analysis identified the structural features that are responsible for Chrimson's red light sensitivity; namely, the protonation of the counterion for the retinal Schiff base, and the polar residue distribution and rigidity of the retinal binding pocket. Based on these mechanistic insights, we engineered ChrimsonSA, a mutant with a maximum activation wavelength red-shifted beyond 605 nm and accelerated closing kinetics.
53 schema:genre research_article
54 schema:inLanguage en
55 schema:isAccessibleForFree true
56 schema:isPartOf N3f9826dd97024a3a91e9d1e4e1719b99
57 Ncec2d794700d4395b1d04e6459c14d94
58 sg:journal.1043282
59 schema:name Crystal structure of the red light-activated channelrhodopsin Chrimson
60 schema:pagination 3949
61 schema:productId N581cdff882604d85a97a256f105e3c91
62 N8106ba8617b44f3aa6b9d9980c79a062
63 Nb73ba2bdacfa40258853127097cd3c5a
64 Nc96aedca39194db5b15ec789487e1be3
65 Nff19c5dd04a14d1693533a2b229d0a61
66 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107129366
67 https://doi.org/10.1038/s41467-018-06421-9
68 schema:sdDatePublished 2019-04-10T17:37
69 schema:sdLicense https://scigraph.springernature.com/explorer/license/
70 schema:sdPublisher Nfcecd4b8908245a8a9e37fe02bd51c28
71 schema:url https://www.nature.com/articles/s41467-018-06421-9
72 sgo:license sg:explorer/license/
73 sgo:sdDataset articles
74 rdf:type schema:ScholarlyArticle
75 N089e677466c44c07ac1b94081a34bbde schema:name Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), 20251, Hamburg, Germany
76 rdf:type schema:Organization
77 N1bd0f7f798f849bc814959ce321e280f rdf:first sg:person.01033506435.08
78 rdf:rest Nb280a0a6ef474f5a86da4b832219c0e2
79 N2d4f033ee2114329bce5af0509481d1a rdf:first sg:person.01043223704.15
80 rdf:rest rdf:nil
81 N312766acf3c34ba0b772f859e9eef3e4 rdf:first sg:person.0752316056.01
82 rdf:rest N3d5ebaef7f0947fc874dc88e10242d67
83 N3d5ebaef7f0947fc874dc88e10242d67 rdf:first sg:person.013712103677.26
84 rdf:rest Na7cd8465c46f4b17a64d7e3944cf6cc4
85 N3f9826dd97024a3a91e9d1e4e1719b99 schema:issueNumber 1
86 rdf:type schema:PublicationIssue
87 N4791d6324f9746ed908b4991097b5c12 rdf:first sg:person.0624540116.94
88 rdf:rest N6028d86bfdb64bf5aa1bf9550a2cd470
89 N581cdff882604d85a97a256f105e3c91 schema:name doi
90 schema:value 10.1038/s41467-018-06421-9
91 rdf:type schema:PropertyValue
92 N6028d86bfdb64bf5aa1bf9550a2cd470 rdf:first sg:person.0740613472.98
93 rdf:rest N1bd0f7f798f849bc814959ce321e280f
94 N67bf0827a2cd49f49f97ac5ba96fd4b0 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
95 schema:familyName Oda
96 schema:givenName Kazumasa
97 rdf:type schema:Person
98 N747acd001dad4f96bee72b9a090141dd rdf:first N67bf0827a2cd49f49f97ac5ba96fd4b0
99 rdf:rest N758935aa5e3a4ddb86c5879d444a345f
100 N758935aa5e3a4ddb86c5879d444a345f rdf:first sg:person.01103001460.23
101 rdf:rest N312766acf3c34ba0b772f859e9eef3e4
102 N8106ba8617b44f3aa6b9d9980c79a062 schema:name readcube_id
103 schema:value c0bd25dff50e7b1080c8ee67af21dfb8849b3902202ca05d154a0a0a5b907823
104 rdf:type schema:PropertyValue
105 Na7cd8465c46f4b17a64d7e3944cf6cc4 rdf:first sg:person.0677124351.35
106 rdf:rest N4791d6324f9746ed908b4991097b5c12
107 Nb280a0a6ef474f5a86da4b832219c0e2 rdf:first sg:person.0660723716.59
108 rdf:rest N2d4f033ee2114329bce5af0509481d1a
109 Nb73ba2bdacfa40258853127097cd3c5a schema:name pubmed_id
110 schema:value 30258177
111 rdf:type schema:PropertyValue
112 Nc96aedca39194db5b15ec789487e1be3 schema:name nlm_unique_id
113 schema:value 101528555
114 rdf:type schema:PropertyValue
115 Ncec2d794700d4395b1d04e6459c14d94 schema:volumeNumber 9
116 rdf:type schema:PublicationVolume
117 Nd62b6887622e405b8a4c520d5516b983 schema:name Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg (ZMNH), 20251, Hamburg, Germany
118 rdf:type schema:Organization
119 Ne1141e2c3be144f5bbf43360455791e4 schema:name RIKEN SPring-8 Center, 679-5198, Sayo, Japan
120 rdf:type schema:Organization
121 Nfcecd4b8908245a8a9e37fe02bd51c28 schema:name Springer Nature - SN SciGraph project
122 rdf:type schema:Organization
123 Nff19c5dd04a14d1693533a2b229d0a61 schema:name dimensions_id
124 schema:value pub.1107129366
125 rdf:type schema:PropertyValue
126 anzsrc-for:02 schema:inDefinedTermSet anzsrc-for:
127 schema:name Physical Sciences
128 rdf:type schema:DefinedTerm
129 anzsrc-for:0299 schema:inDefinedTermSet anzsrc-for:
130 schema:name Other Physical Sciences
131 rdf:type schema:DefinedTerm
132 sg:grant.6504146 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-018-06421-9
133 rdf:type schema:MonetaryGrant
134 sg:grant.6534916 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-018-06421-9
135 rdf:type schema:MonetaryGrant
136 sg:grant.6822921 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-018-06421-9
137 rdf:type schema:MonetaryGrant
138 sg:grant.6825069 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-018-06421-9
139 rdf:type schema:MonetaryGrant
140 sg:journal.1043282 schema:issn 2041-1723
141 schema:name Nature Communications
142 rdf:type schema:Periodical
143 sg:person.01033506435.08 schema:affiliation https://www.grid.ac/institutes/grid.419082.6
144 schema:familyName Nishizawa
145 schema:givenName Tomohiro
146 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01033506435.08
147 rdf:type schema:Person
148 sg:person.01043223704.15 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
149 schema:familyName Nureki
150 schema:givenName Osamu
151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043223704.15
152 rdf:type schema:Person
153 sg:person.01103001460.23 schema:affiliation https://www.grid.ac/institutes/grid.7468.d
154 schema:familyName Vierock
155 schema:givenName Johannes
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01103001460.23
157 rdf:type schema:Person
158 sg:person.013712103677.26 schema:affiliation Nd62b6887622e405b8a4c520d5516b983
159 schema:familyName Rodriguez-Rozada
160 schema:givenName Silvia
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013712103677.26
162 rdf:type schema:Person
163 sg:person.0624540116.94 schema:affiliation Ne1141e2c3be144f5bbf43360455791e4
164 schema:familyName Yamashita
165 schema:givenName Keitaro
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0624540116.94
167 rdf:type schema:Person
168 sg:person.0660723716.59 schema:affiliation https://www.grid.ac/institutes/grid.7468.d
169 schema:familyName Hegemann
170 schema:givenName Peter
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0660723716.59
172 rdf:type schema:Person
173 sg:person.0677124351.35 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
174 schema:familyName Taniguchi
175 schema:givenName Reiya
176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0677124351.35
177 rdf:type schema:Person
178 sg:person.0740613472.98 schema:affiliation N089e677466c44c07ac1b94081a34bbde
179 schema:familyName Wiegert
180 schema:givenName J. Simon
181 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0740613472.98
182 rdf:type schema:Person
183 sg:person.0752316056.01 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
184 schema:familyName Oishi
185 schema:givenName Satomi
186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0752316056.01
187 rdf:type schema:Person
188 sg:pub.10.1007/s00239-003-2557-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033133304
189 https://doi.org/10.1007/s00239-003-2557-8
190 rdf:type schema:CreativeWork
191 sg:pub.10.1038/nature06977 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051651970
192 https://doi.org/10.1038/nature06977
193 rdf:type schema:CreativeWork
194 sg:pub.10.1038/nature10360 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030639357
195 https://doi.org/10.1038/nature10360
196 rdf:type schema:CreativeWork
197 sg:pub.10.1038/nature10870 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025722569
198 https://doi.org/10.1038/nature10870
199 rdf:type schema:CreativeWork
200 sg:pub.10.1038/ncomms8177 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017651708
201 https://doi.org/10.1038/ncomms8177
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/nmeth.2836 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030668007
204 https://doi.org/10.1038/nmeth.2836
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nn.2120 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042891337
207 https://doi.org/10.1038/nn.2120
208 rdf:type schema:CreativeWork
209 sg:pub.10.1038/nn.2247 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028782300
210 https://doi.org/10.1038/nn.2247
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/nn.3502 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037754750
213 https://doi.org/10.1038/nn.3502
214 rdf:type schema:CreativeWork
215 sg:pub.10.1038/nn1525 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043162871
216 https://doi.org/10.1038/nn1525
217 rdf:type schema:CreativeWork
218 sg:pub.10.1038/s41467-018-04146-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103640980
219 https://doi.org/10.1038/s41467-018-04146-3
220 rdf:type schema:CreativeWork
221 sg:pub.10.1038/s41598-017-09600-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091344499
222 https://doi.org/10.1038/s41598-017-09600-8
223 rdf:type schema:CreativeWork
224 sg:pub.10.1038/srep14807 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015762844
225 https://doi.org/10.1038/srep14807
226 rdf:type schema:CreativeWork
227 sg:pub.10.1186/1472-6807-8-49 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017381549
228 https://doi.org/10.1186/1472-6807-8-49
229 rdf:type schema:CreativeWork
230 https://app.dimensions.ai/details/publication/pub.1082780994 schema:CreativeWork
231 https://doi.org/10.1002/jcc.21663 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017943993
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1002/prot.20744 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009285243
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1016/j.bbabio.2013.09.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024378839
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1016/j.bbabio.2013.10.014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005868184
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1016/j.bbagen.2014.05.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041093715
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1016/j.bpj.2014.03.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010378023
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1016/j.jmb.2014.11.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006355659
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1016/s0006-3495(94)80587-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030370402
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1021/bi901634p schema:sameAs https://app.dimensions.ai/details/publication/pub.1008609531
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1039/b815762f schema:sameAs https://app.dimensions.ai/details/publication/pub.1047567618
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1073/pnas.1523341113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025957146
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1073/pnas.1936192100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001065397
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1074/jbc.m111.326207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013231754
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1074/jbc.m112.391185 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051835585
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1101/pdb.prot094888 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083403746
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1101/pdb.prot094904 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083403748
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1107/s0907444904023510 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033689976
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1107/s0907444909047337 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032162623
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1107/s0907444909052925 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020777046
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1107/s0907444910007493 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000235100
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1107/s2059798318004576 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103628910
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1111/j.1751-1097.2011.01027.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1049770281
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1111/php.12741 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085403101
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1126/science.1072068 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047484856
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1126/science.1249375 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044788697
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1126/science.1252367 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049887715
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1126/science.aah3497 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051924025
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1126/science.aan5544 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091782644
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1126/science.aan8862 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092934582
288 rdf:type schema:CreativeWork
289 https://doi.org/10.1371/journal.pone.0119558 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001185730
290 rdf:type schema:CreativeWork
291 https://doi.org/10.3791/55497 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085625508
292 rdf:type schema:CreativeWork
293 https://www.grid.ac/institutes/grid.26999.3d schema:alternateName University of Tokyo
294 schema:name Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan
295 rdf:type schema:Organization
296 https://www.grid.ac/institutes/grid.419082.6 schema:alternateName Japan Science and Technology Agency
297 schema:name Department of Biological Sciences Graduate School of Science, The University of Tokyo, 113-0034, Tokyo, Japan
298 Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 332-0012, Kawaguchi, Japan
299 rdf:type schema:Organization
300 https://www.grid.ac/institutes/grid.7468.d schema:alternateName Humboldt University of Berlin
301 schema:name Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
302 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...