9O4J

Cryo-EM Structure of the Arabidopsis GA3-GID1A-RGA Complex

Summary for 9O4J

• Entry DOI: 10.2210/pdb9o4j/pdb
• EMDB information: 70103
• Descriptor: DELLA protein RGA, Gibberellin receptor GID1A, GIBBERELLIN A3 (3 entities in total)
• Functional Keywords: rga, gid1a, della, arabidopsis, plant protein
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 2
• Total formula weight: 105375.54

Authors

Dahal, P.,Sharma, K.,Borgnia, M.,Zhou, P. (deposition date: 2025-04-08, release date: 2025-07-23, Last modification date: 2025-08-20)

Primary citation

Dahal, P.,Wang, Y.,Hu, J.,Park, J.,Forker, K.,Zhang, Z.L.,Sharma, K.,Borgnia, M.J.,Sun, T.P.,Zhou, P.
Structural insights into proteolysis-dependent and -independent suppression of the master regulator DELLA by the gibberellin receptor.
Proc.Natl.Acad.Sci.USA, 122:e2511012122-e2511012122, 2025

PubMed Abstract: The perception of the phytohormone gibberellin (GA) by its nuclear receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) triggers polyubiquitination and proteasomal degradation of master growth regulators-DELLA proteins-mediated by the SCF E3 ubiquitin ligase complex. DELLA-encoding genes are known as 'Green Revolution' genes, as their dominant mutations lead to semidwarf cereal varieties with significantly higher yields due to reduced GA response. DELLAs function as central signaling hubs, coordinating diverse physiological responses by interacting with key transcription factors across multiple cellular pathways. While the DELLA domain mediates GA-GID1 binding, the mechanism of SCF recruitment remained unknown. Additionally, GA-GID1 binding can inhibit DELLA protein activity independently of its proteolysis, although the underlying mechanism was unclear. Here, we present the cryo-EM structures of GA-GID1A complexed with a full-length DELLA protein in , RGA (REPRESSOR OF ), and the GA-GID1A-RGA-SLY1-ASK1 complex. We show that the DELLA domain of RGA functions as a molecular bridge to enhance its GRAS domain binding to GID1A through direct interactions with both the GRAS domain and GID1A. Disrupting either intramolecular (DELLA-GRAS) or intermolecular (GRAS-GID1A) interactions weakens RGA-GID1 binding. Contrary to prior models, SLY1 binds the GRAS domain's concave surface without inducing conformational changes. Combining AlphaFold modeling and yeast three-hybrid assays, we demonstrate that GID1 binding to the RGA GRAS domain blocks its interactions with INDETERMINATE DOMAIN (IDD) transcription factors, explaining how GA-GID1 relieves growth suppression independently of DELLA degradation.

PubMed: 40768360
DOI: 10.1073/pnas.2511012122

Experimental method

ELECTRON MICROSCOPY (3.06 Å)