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Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.<\/jats:p>","DOI":"10.1126\/sciadv.adp2665","type":"journal-article","created":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T17:58:47Z","timestamp":1748455127000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":6,"title":["Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes"],"prefix":"10.1126","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6727-8395","authenticated-orcid":true,"given":"Luisa","family":"Sauthof","sequence":"first","affiliation":[{"name":"Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charit\u00e9platz 1, D-10117, Berlin, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5079-6893","authenticated-orcid":true,"given":"Michal","family":"Szczepek","sequence":"additional","affiliation":[{"name":"Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charit\u00e9platz 1, D-10117, Berlin, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1985-1908","authenticated-orcid":true,"given":"Andrea","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charit\u00e9platz 1, D-10117, Berlin, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6154-6635","authenticated-orcid":true,"given":"Asmit","family":"Bhowmick","sequence":"additional","affiliation":[{"name":"Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2509-3699","authenticated-orcid":true,"given":"Medhanjali","family":"Dasgupta","sequence":"additional","affiliation":[{"name":"Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4913-0848","authenticated-orcid":true,"given":"Megan J.","family":"Mackintosh","sequence":"additional","affiliation":[{"name":"Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8920-8737","authenticated-orcid":true,"given":"Sheraz","family":"Gul","sequence":"additional","affiliation":[{"name":"Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franklin D.","family":"Fuller","sequence":"additional","affiliation":[{"name":"Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA."},{"name":"Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS103, Menlo Park, CA 94025, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruchira","family":"Chatterjee","sequence":"additional","affiliation":[{"name":"Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4713-9504","authenticated-orcid":true,"given":"Iris D.","family":"Young","sequence":"additional","affiliation":[{"name":"Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6722-416X","authenticated-orcid":true,"given":"Norbert","family":"Michael","sequence":"additional","affiliation":[{"name":"Technische Universit\u00e4t Berlin, Institut f\u00fcr Chemie, Sekr. 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