9IRK

Cryo-EM structure of PhyB(Y276H,1-908)-PIF6beta complex

Summary for 9IRK

• Entry DOI: 10.2210/pdb9irk/pdb
• EMDB information: 60816
• Descriptor: Phytochrome B, Transcription factor PIF6, 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: pif6-mediated, red light, signal transduction, phytochrome b, gene regulation
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 3
• Total formula weight: 220085.77

Authors

Jia, H.L.,Guan, Z.Y.,Ding, J.Y.,Wang, X.Y.,Ma, L.,Yin, P. (deposition date: 2024-07-16, release date: 2025-06-04)

Primary citation

Jia, H.,Guan, Z.,Ding, J.,Wang, X.,Tian, D.,Zhu, Y.,Zhang, D.,Liu, Z.,Ma, L.,Yin, P.
Structural insight into PIF6-mediated red light signal transduction of plant phytochrome B.
Cell Discov, 11:51-51, 2025

PubMed Abstract: The red/far-red light receptor phytochrome B (phyB) plays essential roles in regulating various plant development processes. PhyB exists in two distinct photoreversible forms: the inactive Pr form and the active Pfr form. phyB-Pfr binds phytochrome-interacting factors (PIFs) to transduce red light signals. Here, we determined the cryo-electron microscopy (cryo-EM) structures of the photoactivated phyB-Pfr‒PIF6 complex, the constitutively active mutant phyB‒PIF6 complex, and the truncated phyBN‒PIF6 complex. In these structures, two parallel phyB-Pfr molecules interact with one PIF6 molecule. Red light-triggered rotation of the PΦB D-ring leads to the conversion of hairpin loops into α helices and the "head-to-head" reassembly of phyB-Pfr N-terminal photosensory modules. The interaction between phyB-Pfr and PIF6 influences the dimerization and transcriptional activation activity of PIF6, and PIF6 stabilizes the N-terminal extension of phyB-Pfr and increases the Pr→Pfr photoconversion efficiency of phyB. Our findings reveal the molecular mechanisms underlying Pr→Pfr photoconversion and PIF6-mediated red light signal transduction of phyB.

PubMed: 40404641
DOI: 10.1038/s41421-025-00802-3

Experimental method

ELECTRON MICROSCOPY (2.8 Å)