7RZW

CryoEM structure of Arabidopsis thaliana phytochrome B

Summary for 7RZW

• Entry DOI: 10.2210/pdb7rzw/pdb
• EMDB information: 24780
• Descriptor: Phytochrome B, 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 (2 entities in total)
• Functional Keywords: phytochrome, asymmetric dimer, gene regulation
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 2
• Total formula weight: 260119.45

Authors

Li, H.,Burgie, E.S.,Vierstra, R.D.,Li, H. (deposition date: 2021-08-27, release date: 2022-04-13, Last modification date: 2022-04-20)

Primary citation

Li, H.,Burgie, E.S.,Gannam, Z.T.K.,Li, H.,Vierstra, R.D.
Plant phytochrome B is an asymmetric dimer with unique signalling potential.
Nature, 604:127-133, 2022

PubMed Abstract: Many aspects of plant photoperception are mediated by the phytochrome (Phy) family of bilin-containing photoreceptors that reversibly interconvert between inactive Pr and active Pfr conformers. Despite extensive biochemical studies, full understanding of plant Phy signalling has remained unclear due to the absence of relevant 3D models. Here we report a cryo-electron microscopy structure of Arabidopsis PhyB in the Pr state that reveals a topologically complex dimeric organization that is substantially distinct from its prokaryotic relatives. Instead of an anticipated parallel architecture, the C-terminal histidine-kinase-related domains (HKRDs) associate head-to-head, whereas the N-terminal photosensory regions associate head-to-tail to form a parallelogram-shaped platform with near two-fold symmetry. The platform is internally linked by the second of two internal Per/Arnt/Sim domains that binds to the photosensory module of the opposing protomer and a preceding 'modulator' loop that assembles tightly with the photosensory module of its own protomer. Both connections accelerate the thermal reversion of Pfr back to Pr, consistent with an inverse relationship between dimer assembly and Pfr stability. Lopsided contacts between the HKRDs and the platform create profound asymmetry to PhyB that might imbue distinct signalling potentials to the protomers. We propose that this unique structural dynamism creates an extensive photostate-sensitive surface for conformation-dependent interactions between plant Phy photoreceptors and their signalling partners.

PubMed: 35355010
DOI: 10.1038/s41586-022-04529-z

Experimental method

ELECTRON MICROSCOPY (3.3 Å)