8YB4

Pfr conformer of Arabidopsis thaliana phytochrome B in complex with phytochrome-interacting factor 6

Summary for 8YB4

• Entry DOI: 10.2210/pdb8yb4/pdb
• EMDB information: 39108
• Descriptor: phytochrome B, phytochrome-interacting factor 6, 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid (3 entities in total)
• Functional Keywords: phytochrome, phytochrome interaction factor, signal complex, signaling protein, gene regulation
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 3
• Total formula weight: 272630.42

Authors

Wang, Z.,Wang, W.,Zhao, D.,Song, Y.,Xu, B.,Zhao, J.,Wang, J. (deposition date: 2024-02-11, release date: 2024-10-02, Last modification date: 2024-10-09)

Primary citation

Wang, Z.,Wang, W.,Zhao, D.,Song, Y.,Lin, X.,Shen, M.,Chi, C.,Xu, B.,Zhao, J.,Deng, X.W.,Wang, J.
Light-induced remodeling of phytochrome B enables signal transduction by phytochrome-interacting factor.
Cell, 2024

PubMed Abstract: Phytochrome B (phyB) and phytochrome-interacting factors (PIFs) constitute a well-established signaling module critical for plants adapting to ambient light. However, mechanisms underlying phyB photoactivation and PIF binding for signal transduction remain elusive. Here, we report the cryo-electron microscopy (cryo-EM) structures of the photoactivated phyB or the constitutively active phyB mutant in complex with PIF6, revealing a similar trimer. The light-induced configuration switch of the chromophore drives a conformational transition of the nearby tongue signature within the phytochrome-specific (PHY) domain of phyB. The resulting α-helical PHY tongue further disrupts the head-to-tail dimer of phyB in the dark-adapted state. These structural remodelings of phyB facilitate the induced-fit recognition of PIF6, consequently stabilizing the N-terminal extension domain and a head-to-head dimer of activated phyB. Interestingly, the phyB dimer exhibits slight asymmetry, resulting in the binding of only one PIF6 molecule. Overall, our findings solve a key question with respect to how light-induced remodeling of phyB enables PIF signaling in phytochrome research.

PubMed: 39317197
DOI: 10.1016/j.cell.2024.09.005

Experimental method

ELECTRON MICROSCOPY (3.1 Å)