Evidence map›Paper›PMID 40544164›Full record

ArticleNature communications2025

Pr and Pfr structures of plant phytochrome A.

Soshichiro Nagano, David von Stetten, Kaoling Guan, Peng-Yuan Chen, Chen Song, Thomas Barends, Manfred S Weiss, Christian G Feiler, Katerina Dörner, Iñaki de Diego Martinez and 22 more

Erratum issuedAbstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Circular dichroism spectroscopy reveals multiple phytochrome photoproducts in equilibrium.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

32 authors.

Soshichiro Nagano *Institute for Plant Physiology, Justus Liebig University, Giessen, Germany. soshichiro.nagano@mr.mpg.de.ORCID http://orcid.org/0000-0002-3080-6019
David von Stetten *European Molecular Biology Laboratory (EMBL), Hamburg, Germany.ORCID http://orcid.org/0000-0001-7906-9788
Kaoling Guan *Institute for Plant Physiology, Justus Liebig University, Giessen, Germany.ORCID http://orcid.org/0000-0001-6530-3705
Peng-Yuan ChenInstitute for Plant Physiology, Justus Liebig University, Giessen, Germany.ORCID http://orcid.org/0000-0002-6444-4933
Chen SongDepartment of Analytical Chemistry, University of Leipzig, Leipzig, Germany.ORCID http://orcid.org/0000-0003-1034-5881
Thomas BarendsDepartment of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany.
Manfred S WeissHelmholtz-Zentrum Berlin für Materialien und Energie, BESSY II, Macromolecular Crystallography, Berlin, Germany.ORCID http://orcid.org/0000-0002-2362-7047
Christian G FeilerHelmholtz-Zentrum Berlin für Materialien und Energie, BESSY II, Macromolecular Crystallography, Berlin, Germany.
Katerina DörnerEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0003-1072-5905
Iñaki de Diego MartinezEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-6156-4032
Robin SchubertEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-6213-2872
Johan BieleckiEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-3012-603X
Lea BringsEuropean XFEL GmbH, Schenefeld, Germany.
Huijong HanEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-1197-3014
Konstantin KharitonovEuropean XFEL GmbH, Schenefeld, Germany.
Chan KimEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0003-4559-7982
Marco KloosEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-8745-9740
Jayanath C P KoliyaduEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-0245-3842
Faisal H M KouaEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0001-8371-9587
Ekaterina RoundEuropean XFEL GmbH, Schenefeld, Germany.
Abhisakh SarmaEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-0785-8902
Tokushi SatoEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0003-3155-3487
Christina SchmidtEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-6662-1294
Joana ValerioEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0001-5931-0925
Agnieszka WronaEuropean XFEL GmbH, Schenefeld, Germany.
Joachim SchulzEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-9310-8832
Raphael de WijnEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-8342-1008
Romain LetrunEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0002-0569-5193
Richard BeanEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0001-8151-7439
Adrian MancusoEuropean XFEL GmbH, Schenefeld, Germany.ORCID http://orcid.org/0000-0003-1710-8969
Karsten HeyneDepartment of Physics, Free University of Berlin, Berlin, Germany.
Jon HughesInstitute for Plant Physiology, Justus Liebig University, Giessen, Germany. jon.hughes@uni-giessen.de.ORCID http://orcid.org/0000-0001-6070-004X

Funding

Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research) 05K16GU1, 05K19GU1, 05K22GU6Deutsche Forschungsgemeinschaft (German Research Foundation) SFB1078/B7Deutsche Forschungsgemeinschaft (German Research Foundation) SFB1078/B7, HU702/9, HU702/12Deutsche Forschungsgemeinschaft (German Research Foundation) SO1785/1Helmholtz Association | Helmholtz-Zentrum Berlin für Materialien und Energie (Helmholtz-Zentrum Berlin) MX-221-00302
6 · The paper itself

Abstract

Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant.

Indexed as

Glycine maxPhytochrome APlant ProteinsCrystallography, X-RayLightModels, MolecularProtein ConformationPhytochrome APlant Proteins

Identifiers

PMID40544164
PMCPMC12182589

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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.