9LUP | pdb_00009lup

Cryo-EM structure of Arabidopsis thaliana RGA in complex with GID1A, SLY1, and ASK2 (composite map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into gibberellin-mediated DELLA protein degradation.

Islam, S.Park, K.Xia, J.Kwon, E.Kim, D.Y.

(2025) Mol Plant 18: 1210-1221

  • DOI: https://doi.org/10.1016/j.molp.2025.06.010
  • Primary Citation of Related Structures:  
    9LUM, 9LUN, 9LUO, 9LUP

  • PubMed Abstract: 

    Gibberellin promotes plant growth by downregulating DELLA proteins, which act as growth repressors. In the presence of gibberellin, the gibberellin receptor GID1 binds DELLA proteins, triggering their degradation through polyubiquitination by the SCF SLY1/GID2 ubiquitin E3 ligase. Despite extensive studies, the molecular mechanisms by which DELLA proteins assemble with SCF SLY1/GID2 to regulate plant growth remain poorly understood. Here, we present two cryo-electron microscopy structures of the Arabidopsis thaliana DELLA protein RGA in complex with GID1A and GID1A-SLY1-ASK2, respectively. Structural analyses revealed that RGA interacts with GID1A and SLY1 through nonoverlapping binding surfaces, stabilizing the proteins. This suggests that the SCF SLY1 -RGA-GID1A complex assembles through a stepwise stabilization process induced by gibberellin. Furthermore, structural comparison with GRAS proteins indicates that RGA does not interact with IDD-family transcription factors when bound to SLY1, suggesting that DELLA protein binding to GID1/SLY1 and to transcription factors is mutually exclusive. These findings provide new insights into the gibberellin-mediated regulation of transcription factor activity by DELLA proteins.


  • Organizational Affiliation
    • College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DELLA protein RGA588Arabidopsis thalianaMutation(s): 0 
Gene Names: RGAGRSRGA1At2g01570F2I9.19
UniProt
Find proteins for Q9SLH3 (Arabidopsis thaliana)
Explore Q9SLH3 
Go to UniProtKB:  Q9SLH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SLH3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gibberellin receptor GID1A347Arabidopsis thalianaMutation(s): 0 
Gene Names: GID1ACXE10GID1L1At3g05120T12H1.8
EC: 3
UniProt
Find proteins for Q9MAA7 (Arabidopsis thaliana)
Explore Q9MAA7 
Go to UniProtKB:  Q9MAA7
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UniProt GroupQ9MAA7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
F-box protein GID2153Arabidopsis thalianaMutation(s): 0 
Gene Names: GID2SLY1At4g24210T22A6.40
UniProt
Find proteins for Q9STX3 (Arabidopsis thaliana)
Explore Q9STX3 
Go to UniProtKB:  Q9STX3
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UniProt GroupQ9STX3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SKP1-like protein 1B173Arabidopsis thalianaMutation(s): 0 
Gene Names: SKP1BASK2UIP2At5g42190MJC20.30
UniProt
Find proteins for Q9FHW7 (Arabidopsis thaliana)
Explore Q9FHW7 
Go to UniProtKB:  Q9FHW7
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UniProt GroupQ9FHW7
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection, Database references