Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Structural insights into photoactivation and signalling in plant phytochromes


Plant phytochromes are red/far-red photochromic photoreceptors that act as master regulators of development, controlling the expression of thousands of genes. Here, we describe the crystal structures of four plant phytochrome sensory modules, three at about 2 Å resolution or better, including the first of an A-type phytochrome. Together with extensive spectral data, these structures provide detailed insight into the structure and function of plant phytochromes. In the Pr state, the substitution of phycocyanobilin and phytochromobilin cofactors has no structural effect, nor does the amino-terminal extension play a significant functional role. Our data suggest that the chromophore propionates and especially the phytochrome-specific domain tongue act differently in plant and prokaryotic phytochromes. We find that the photoproduct in period–ARNT–single-minded (PAS)–cGMP-specific phosphodiesterase–adenylyl cyclase–FhlA (GAF) bidomains might represent a novel intermediate between MetaRc and Pfr. We also discuss the possible role of a likely nuclear localization signal specific to and conserved in the phytochrome A lineage.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: UV–vis absorbance and CD spectra of the seven plant phytochrome constructs investigated.
Fig. 2: Sb.phyB(PG)–PCB 1.8 Å structure (PDB 6TBY).
Fig. 3: Gm.phyB(PGP)–PCB 2.9 Å structure (PDB 6TL4).
Fig. 4: Gm.phyA(PG)–PCB 2.1 Å structure (PDB 6TC7).

Data availability

The three-dimensional structural data that support the findings of this study have been deposited in wwPDB with the accession codes 6TBY, 6TC5, 6TL4 and 6TC7. The authors declare that all other data supporting the findings of this study are available within the paper and its Supplementary Information files.


  1. 1.

    Anders, K., Daminelli-Widany, G., Mroginski, M. A., von Stetten, D. & Essen, L. O. Structure of the cyanobacterial phytochrome 2 photosensor implies a tryptophan switch for phytochrome signaling. J. Biol. Chem. 288, 35714–35725 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Takala, H. et al. Signal amplification and transduction in phytochrome photosensors. Nature 509, 245–248 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Oka, Y. et al. Functional analysis of a 450-amino acid N-terminal fragment of phytochrome B in Arabidopsis. Plant Cell 16, 2104–2116 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Matsushita, T., Mochizuki, N. & Nagatani, A. Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature 424, 571–574 (2003).

    CAS  PubMed  Google Scholar 

  5. 5.

    Qiu, Y. et al. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat. Commun. 8, 1905 (2017).

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    Viczian, A. et al. A short amino-terminal part of Arabidopsis phytochrome A induces constitutive photomorphogenic response. Mol. Plant 5, 629–641 (2012).

    PubMed  Google Scholar 

  7. 7.

    Song, C. et al. 3D structures of plant phytochrome A as Pr and Pfr from solid-state NMR: implications for molecular function. Front. Plant Sci. 9, 498 (2018).

    PubMed  PubMed Central  Google Scholar 

  8. 8.

    Sharrock, R. A. & Quail, P. H. Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 3, 1745–1757 (1989).

    CAS  PubMed  Google Scholar 

  9. 9.

    Rockwell, N. C., Shang, L., Martin, S. S. & Lagarias, J. C. Distinct classes of red/far-red photochemistry within the phytochrome superfamily. Proc. Natl Acad. Sci. USA 106, 6123–6127 (2009).

    CAS  PubMed  Google Scholar 

  10. 10.

    Mailliet, J. et al. Spectroscopy and a high-resolution crystal structure of Tyr263 mutants of cyanobacterial phytochrome Cph1. J. Mol. Biol. 413, 115–127 (2011).

    CAS  PubMed  Google Scholar 

  11. 11.

    Song, C. et al. Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome. Proc. Natl Acad. Sci. USA 108, 3842–3847 (2011).

    CAS  PubMed  Google Scholar 

  12. 12.

    Essen, L.-O., Mailliet, J. & Hughes, J. The structure of a complete phytochrome sensory module in the Pr ground state. Proc. Natl Acad. Sci. USA 105, 14709–14714 (2008).

    CAS  PubMed  Google Scholar 

  13. 13.

    Burgie, E. S., Bussell, A. N., Walker, J. M., Dubiel, K. & Vierstra, R. D. Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc. Natl Acad. Sci. USA 111, 10179–10184 (2014).

    CAS  PubMed  Google Scholar 

  14. 14.

    Kneip, C. et al. Effect of chromophore exchange on the resonance Raman spectra of recombinant phytochromes. FEBS 414, 23–26 (1997).

    CAS  Google Scholar 

  15. 15.

    Remberg, A. et al. Raman spectroscopic and light-induced-kinetic characterization of a recombinant phytochrome of the cyanobacterium Synechocystis. Biochemistry 36, 13389–13395 (1997).

    CAS  PubMed  Google Scholar 

  16. 16.

    Mroginski, M. A. et al. Structure of the chromophore binding pocket in the Pr state of plant phytochrome phyA. J. Phys. Chem. B 115, 1220–1231 (2011).

    CAS  PubMed  Google Scholar 

  17. 17.

    Wahleithner, J. A., Li, L. M. & Lagarias, J. C. Expression and assembly of spectrally active recombinant holophytochrome. Proc. Natl Acad. Sci. USA 88, 10387–10391 (1991).

    CAS  PubMed  Google Scholar 

  18. 18.

    Elich, T. D. & Lagarias, J. C. Formation of a photoreversible phycocyanobilin-apophytochrome adduct in vitro. J. Biol. Chem. 264, 12902–12908 (1989).

    CAS  PubMed  Google Scholar 

  19. 19.

    Song, C., Essen, L. O., Gärtner, W., Hughes, J. & Matysik, J. Solid-state NMR spectroscopic study of chromophore–protein interactions in the Pr ground state of plant phytochrome A. Mol. Plant 5, 698–715 (2012).

    CAS  PubMed  Google Scholar 

  20. 20.

    Velazquez Escobar, F. et al. Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB. FEBS Lett. 591, 1258–1265 (2017).

    CAS  PubMed  Google Scholar 

  21. 21.

    Parker, W., Partis, M. & Song, P. S. N-terminal domain of Avena phytochrome: interactions with sodium dodecyl sulfate micelles and N-terminal chain truncated phytochrome. Biochemistry 31, 9413–9420 (1992).

    CAS  PubMed  Google Scholar 

  22. 22.

    Litts, J. C., Kelly, J. M. & Lagarias, J. C. Structure–function studies on phytochrome: preliminary characterization of highly purified phytochrome from Avena sativa enriched in the 124-kilodalton species. J. Biol. Chem. 258, 11025–11031 (1983).

    CAS  PubMed  Google Scholar 

  23. 23.

    Claesson, E. et al. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser. eLife 9, e53514 (2020).

    PubMed  PubMed Central  Google Scholar 

  24. 24.

    Wagner, J. R., Brunzelle, J. S., Forest, K. T. & Vierstra, R. D. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438, 325–331 (2005).

    CAS  PubMed  Google Scholar 

  25. 25.

    Eilfeld, P. & Rüdiger, W. Absorption spectra of phytochrome intermediates. Z. Naturforsch. 40c, 109–114 (1985).

    CAS  Google Scholar 

  26. 26.

    Kneip, C. et al. Protonation state and structural changes of the tetrapyrrole chromophore during the Pr → Pfr phototransformation of phytochrome: a resonance Raman spectroscopic study. Biochemistry 38, 15185–15192 (1999).

    CAS  PubMed  Google Scholar 

  27. 27.

    Mizutani, Y., Tokutomi, S. & Kitagawa, T. Resonance Raman spectra of the intermediates in phototransformation of large phytochrome: deprotonation of the chromophore in the bleached intermediate. Biochemistry 33, 153–158 (1994).

    CAS  PubMed  Google Scholar 

  28. 28.

    Mroginski, M. A. et al. Elucidating photoinduced structural changes in phytochromes by the combined application of resonance Raman spectroscopy and theoretical methods. J. Mol. Struct. 993, 15–25 (2011).

    CAS  Google Scholar 

  29. 29.

    Ulijasz, A. T. et al. Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversion. J. Biol. Chem. 283, 21251–21266 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Song, C. et al. The D-ring, not the A-ring, rotates in Synechococcus OS-B’ phytochrome. J. Biol. Chem. 289, 2552–2562 (2014).

    CAS  PubMed  Google Scholar 

  31. 31.

    Auldridge, M. E., Satyshur, K. A., Anstrom, D. M. & Forest, K. T. Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein. J. Biol. Chem. 287, 7000–7009 (2012).

    CAS  PubMed  Google Scholar 

  32. 32.

    Ihalainen, J. A. et al. Chromophore–protein interplay during the phytochrome photocycle revealed by step-scan FTIR spectroscopy. J. Am. Chem. Soc. 140, 12396–12404 (2018).

    CAS  PubMed  Google Scholar 

  33. 33.

    Kacprzak, S. et al. Intersubunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by pulsed electron-electron double resonance (PELDOR) between different spin label positions, remain unchanged upon photoconversion. J. Biol. Chem. 292, 7598–7606 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Park, E. et al. Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters. Plant J. 72, 537–546 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Oka, Y., Matsushita, T., Mochizuki, N., Quail, P. H. & Nagatani, A. Mutant screen distinguishes between residues necessary for light-signal perception and signal transfer by phytochrome B. PLoS Genet. 4, e1000158 (2008).

    PubMed  PubMed Central  Google Scholar 

  36. 36.

    Kikis, E. A., Oka, Y., Hudson, M. E., Nagatani, A. & Quail, P. H. Residues clustered in the light-sensing knot of phytochrome B are necessary for conformer-specific binding to signaling partner PIF3. PLoS Genet. 5, e1000352 (2009).

    PubMed  PubMed Central  Google Scholar 

  37. 37.

    Viczian, A., Klose, C., Adam, E. & Nagy, F. New insights of red light-induced development. Plant Cell Environ. 40, 2457–2468 (2017).

    CAS  PubMed  Google Scholar 

  38. 38.

    Burgie, E. S., Zhang, J. & Vierstra, R. D. Crystal structure of Deinococcus phytochrome in the photoactivated state reveals a cascade of structural rearrangements during photoconversion. Structure 24, 448–457 (2016).

    CAS  PubMed  Google Scholar 

  39. 39.

    Yang, X., Kuk, J. & Moffat, K. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. Proc. Natl Acad. Sci. USA 106, 15639–15644 (2009).

    CAS  PubMed  Google Scholar 

  40. 40.

    van Thor, J. J. et al. Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1. Biochemistry 40, 11460–11471 (2001).

    PubMed  Google Scholar 

  41. 41.

    Borucki, B. et al. Light-induced proton release of phytochrome is coupled to the transient deprotonation of the tetrapyrrole chromophore. J. Biol. Chem. 280, 34358–34364 (2005).

    CAS  PubMed  Google Scholar 

  42. 42.

    Viczian, A. et al. Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling. New Phytol. 225, 1635–1650 (2020).

    CAS  PubMed  Google Scholar 

  43. 43.

    Remberg, A., Ruddat, A., Braslavsky, S. E., Gärtner, W. & Schaffner, K. Chromophore incorporation, Pr to Pfr kinetics, and Pfr thermal reversion of recombinant N-terminal fragments of phytochrome A and B chromoproteins. Biochemistry 37, 9983–9990 (1998).

    CAS  PubMed  Google Scholar 

  44. 44.

    Cherry, J. R., Hondred, D., Walker, J. M. & Vierstra, R. D. Phytochrome requires the 6-kDa N-terminal domain for full biological activity. Proc. Natl Acad. Sci. USA 89, 5039–5043 (1992).

    CAS  PubMed  Google Scholar 

  45. 45.

    Sweere, U. et al. Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling. Science 294, 1108–1111 (2001).

    CAS  PubMed  Google Scholar 

  46. 46.

    Kosugi, S. et al. Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J. Biol. Chem. 284, 478–485 (2009).

    CAS  PubMed  Google Scholar 

  47. 47.

    Mathews, S., Lavin, M. & Sharrock, R. A. Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms. Ann. Missouri Bot. Gard. 82, 296–321 (1995).

    Google Scholar 

  48. 48.

    Chen, M. & Chory, J. Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol. 21, 664–671 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Zeidler, M., Zhou, Q., Sarda, X., Yau, C. P. & Chua, N. H. The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals. Plant J. 40, 355–365 (2004).

    CAS  PubMed  Google Scholar 

  50. 50.

    Oka, Y. et al. Arabidopsis phytochrome A is modularly structured to integrate the multiple features that are required for a highly sensitized phytochrome. Plant Cell 24, 2949–2962 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Song, C. et al. On the collective nature of phytochrome photoactivation. Biochemistry 50, 10987–10989 (2011).

    CAS  PubMed  Google Scholar 

  52. 52.

    Kim, P. W. et al. Unraveling the primary isomerization dynamics in cyanobacterial phytochrome Cph1 with multi-pulse manipulations. J. Phys. Chem. Lett. 4, 2605–2609 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Gustavsson, E. et al. Modulation of structural heterogeneity controls phytochrome photoswitching. Biophys. J. 118, 415–421 (2020).

    CAS  PubMed  Google Scholar 

  54. 54.

    Takala, H. et al. On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome. J. Biol. Chem. 293, 8161–8172 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Al-Sady, B., Ni, W. M., Kircher, S., Schäfer, E. & Quail, P. H. Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasorne-mediated degradation. Mol. Cell 23, 439–446 (2006).

    CAS  PubMed  Google Scholar 

  56. 56.

    Khanna, R. et al. A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. Plant Cell 16, 3033–3044 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Landgraf, F. T., Forreiter, C., Hurtado, P. A., Lamparter, T. & Hughes, J. Recombinant holophytochrome in Escherichia coli. FEBS Lett. 508, 459–462 (2001).

    CAS  PubMed  Google Scholar 

  58. 58.

    Hirose, Y. et al. Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle. Proc. Natl Acad. Sci. USA 110, 4974–4979 (2013).

    CAS  PubMed  Google Scholar 

  59. 59.

    Zhao, K. H. & Scheer, H. Type I and type II reversible photochemistry of phycoerythrocyanin α-subunit from Mastigocladus laminosus both involve Z–E isomerization of phycoviolobilin chromophore and are controlled by sulfhydryls in apoprotein. Biochim. Biophys. Acta Bioenerg. 1228, 244–253 (1995).

    Google Scholar 

  60. 60.

    Ishizuka, T., Narikawa, R., Kohchi, T., Katayama, M. & Ikeuchi, M. Cyanobacteriochrome TePixJ of Thermosynechococcus elongatus harbors phycoviolobilin as a chromophore. Plant Cell Physiol. 48, 1385–1390 (2007).

    CAS  PubMed  Google Scholar 

  61. 61.

    Brandlmeier, T., Scheer, H. & Rudiger, W. Chromophore content and molar absorptivity of phytochrome in the Pr form. Z. Naturforsch. C 36, 431–439 (1981).

    Google Scholar 

  62. 62.

    Fernandez Lopez, M. et al. Role of the propionic side chains for the photoconversion of bacterial phytochromes. Biochemistry 58, 3504–3519 (2019).

    CAS  PubMed  Google Scholar 

  63. 63.

    Mailliet, J. et al. Dwelling in the dark: procedures for the crystallography of phytochromes and other photochromic proteins. Acta Crystallogr. D 65, 1232–1235 (2009).

    CAS  PubMed  Google Scholar 

  64. 64.

    Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).

    CAS  PubMed  Google Scholar 

  65. 65.

    Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013).

    CAS  PubMed  Google Scholar 

  66. 66.

    Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011).

    CAS  PubMed  Google Scholar 

  67. 67.

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Emsley, P. B., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

    CAS  PubMed  Google Scholar 

  69. 69.

    Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011).

    CAS  PubMed  Google Scholar 

  70. 70.

    Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    CAS  Google Scholar 

  71. 71.

    Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).

    CAS  PubMed  Google Scholar 

  72. 72.

    Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 42, 339–341 (2009).

    CAS  Google Scholar 

Download references


We thank SFB 1078 for funding (subprojects B6 to P.H. and B8 to J.H.). The X-ray diffraction measurements were carried out at BL14.1 at BESSY II (Helmholtz-Zentrum Berlin für Materialien und Energie (HZB)) and at ID30-A3 at ESRF with support from CALIPSOplus (Grant Agreement 730872 of the EU Framework Programme HORIZON 2020) and HZB. We thank L.-O. Essen (University of Marburg) for collaboration in the early stages of the project, W. Wende (Giessen) for cooperation in measuring the CD spectra and C. Lang (Giessen) for expert technical assistance. We dedicate this paper to the memory of Winslow Briggs.

Author information




S.N., G.K. and S.M.S. designed, cloned, expressed, purified and crystallized the holophytochrome constructs. S.N. solved the structures with suggestions from C.F. and M.W. S.N. and J.H. interpreted the structures. A.K., D.B. and P.H. measured and interpreted the vibrational spectra. J.H. wrote the manuscript with the participation of P.H. and in discussion with all authors. J.H. devised and co-ordinated the project.

Corresponding author

Correspondence to Jon Hughes.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 RR and IR difference spectra of phyA and phyB constructs.

Left, Sorghum bicolor; Right Glycine max. Above: RR spectra of the Pr states (blue traces) and their photoconversion products (red traces) obtained upon 670 and 750 nm irradiation at ambient temperature. All spectra were measured at 90 K with 1064 nm excitation. The spectral regions labelled are indicative of (i) the methine bridge configurations and conformations (C=C stretching modes of the A-B and C-D methine bridges at ca. 1600–1650 cm−1), (ii) pyrrole nitrogen protonation state (N-H in-plane bending modes of rings B and C at ca. 1550 – 1580 cm−1) and (iii) the C-D methine bridge torsion (hydrogen-out-of-plane [HOOP] mode at ca. 795 - 825 cm−1). The broad feature at ca. 1460 cm−1 is largely due to non-resonant Raman bands of the protein. The high intensity of this feature relative to the RR bands of the chromophore indicates that the latter experience a low resonance enhancement. Below: IR “photoproduct minus Pr” difference spectra obtained upon irradiation with 670 and 750 nm at ambient temperature. The positive signals indicated by black lines and labels refer to the photoproduct, whereas the grey lines and labels mark the signals of the Pr state. Representative spectra based on at least two samples are shown. Spectra for each sample were measured several times. Each spectrum is based on 1000 separate FT scans.

Extended Data Fig. 2 Sb.phyB(PG)-PCB and -PΦB structures are almost identical.

Above: Superimposition of peptide chains with chromophores. The N- and C-termini, the two unresolved loops and the somewhat deviant R234-D236 regions are labelled. Inset: superimposition of the PCB (cyan) and P(B (green) D rings. Below: Chemical structures of PCB, PΦB, and the incorrect model used in 4OUR (PDB cofactor codes CYC, O6E and 2VO, respectively). Note that the uncharged structures are shown, whereas in both Pr and Pfr holoprotein states all four cofactor nitrogens are protonated.

Extended Data Fig. 3 Gm.phyA(PG)-PCB 2.1 Å structure (PDB 6TC7) of subunit B.

PCB (cyan), PAS (slate), GAF (gold), PCB (cyan), waters (red spheres). PW, pyrrole water. Subunit A (grey) is superimposed.

Extended Data Fig. 4 Gm.phyA(PG)-PCB 2.1 Å structure (PDB 6TC7) of subunit B including side chains and hydrogen bonding network.

Note that the weak (3.1 Å) D-ring carbonyl – H370 hydrogen bond in subunit B is somewhat stronger (3.0 Å) in subunit A. PCB (cyan), PAS (slate), GAF (gold), PCB (cyan), waters (red spheres). PW, pyrrole water.

Extended Data Fig. 5 Putative Class I NLS specific to A-type plant phytochromes.

Above. Superimposition of Gm.phyA(PG)-PCB subunit B (GAF domain, gold) with subunit A (grey) superimposed. Although the more mobile N-terminal section of the “380s” loop is missing (gold dashes), the final triad of the putative NLS (R360-R362) is resolved. Below. Alignment of the “380s” loop region in plant phytochromes (from Mathews et al. 47). sm, Selaginella martensii; cp, Ceratodon purpureus; ac, Adiantum caperis-veneris; atA-D, Arabidopsis thaliana PHYA-D; cpA, Curcurbita pepo PHYA; psA, Pisum sativum PHYA; stA/B, Solanum tuberosum PHYA/B, asA-D, Avena sativa PHYA; osA/B, Oryza sativa PHYA/B; zmA, Zea mais PHYA. The K(R/K)K(R/K) consensus is boxed red.

Supplementary information

Supplementary Information

Supplementary Figs. 1–3, Tables 1 and 2, and references.

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Nagano, S., Guan, K., Shenkutie, S.M. et al. Structural insights into photoactivation and signalling in plant phytochromes. Nat. Plants 6, 581–588 (2020).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing