9O4J | pdb_00009o4j

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

• PDB DOI: https://doi.org/10.2210/pdb9O4J/pdb
• EM Map EMD-70103: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-04-08 Released: 2025-07-23 
• Deposition Author(s): Dahal, P., Sharma, K., Borgnia, M., Zhou, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structural Insights into Proteolysis-Dependent and -Independent Suppression of the Master Regulator DELLA by Gibberellin Receptor

Dahal, P., Wang, Y., Hu, J., Park, J., Forker, K., Zhang, Z., Sharma, K., Borgnia, M., Sun, T.P., Zhou, P.

(2025) Proc Natl Acad Sci U S A 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 105.38 kDa 
• Atom Count: 5,958 
• Modeled Residue Count: 781 
• Deposited Residue Count: 952 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELLA protein RGA	A	597	Arabidopsis thaliana	Mutation(s): 3  Gene Names: RGA, GRS, RGA1, At2g01570, F2I9.19
UniProt
Find proteins for Q9SLH3 (Arabidopsis thaliana) Explore Q9SLH3  Go to UniProtKB:  Q9SLH3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gibberellin receptor GID1A	B	355	Arabidopsis thaliana	Mutation(s): 0  Gene Names: GID1A, CXE10, GID1L1, At3g05120, T12H1.8 EC: 3
UniProt
Find proteins for Q9MAA7 (Arabidopsis thaliana) Explore Q9MAA7  Go to UniProtKB:  Q9MAA7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GA3	C [auth B]	GIBBERELLIN A3 C19 H22 O6 IXORZMNAPKEEDV-OBDJNFEBSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Dahal, P., Sharma, K., Borgnia, M., Zhou, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release