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- PDB-9oi8: Cryo-EM Structure of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Comp... -

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Basic information

Entry
Database: PDB / ID: 9oi8
TitleCryo-EM Structure of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Complex (Alternative Conformation)
Components
  • DELLA protein RGA
  • F-box protein GID2
  • Gibberellin receptor GID1A
  • SKP1-like protein 1A
KeywordsPLANT PROTEIN / RGA / DELLA / GID1 / SLY1 / ASK1 / GA
Function / homology
Function and homology information


regulation of gibberellic acid mediated signaling pathway / fruit morphogenesis / gibberellin mediated signaling pathway / positive regulation of gibberellic acid mediated signaling pathway / floral organ morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / gibberellin binding ...regulation of gibberellic acid mediated signaling pathway / fruit morphogenesis / gibberellin mediated signaling pathway / positive regulation of gibberellic acid mediated signaling pathway / floral organ morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / gibberellin binding / seed dormancy process / negative regulation of gibberellic acid mediated signaling pathway / positive regulation of fertilization / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway / phragmoplast / regulation of seed germination / seed germination / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to far red light / Hydrolases / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / negative regulation of DNA recombination / SCF ubiquitin ligase complex / regulation of protein catabolic process / response to cold / chromosome segregation / promoter-specific chromatin binding / microtubule cytoskeleton organization / spindle / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / hydrolase activity / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
F-box protein SNE / Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile. / : / F-box domain ...F-box protein SNE / Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile. / : / F-box domain / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / Alpha/beta hydrolase fold-3 / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / alpha/beta hydrolase fold / F-box domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
GIBBERELLIN A3 / SKP1-like protein 1A / Gibberellin receptor GID1A / DELLA protein RGA / F-box protein GID2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsDahal, P. / Sharma, K. / Borgnia, M. / Zhou, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural insights into proteolysis-dependent and -independent suppression of the master regulator DELLA by the gibberellin receptor.
Authors: Pawan Dahal / Yan Wang / Jianhong Hu / Jeongmoo Park / Karly Forker / Zhong-Lin Zhang / Kedar Sharma / Mario J Borgnia / Tai-Ping Sun / Pei Zhou /
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- ...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.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELLA protein RGA
B: Gibberellin receptor GID1A
C: F-box protein GID2
D: SKP1-like protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7195
Polymers147,3734
Non-polymers3461
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DELLA protein RGA / GAI-related sequence / GRAS family protein 10 / AtGRAS-10 / Repressor on the ga1-3 mutant / ...GAI-related sequence / GRAS family protein 10 / AtGRAS-10 / Repressor on the ga1-3 mutant / Restoration of growth on ammonia protein 1


Mass: 65253.309 Da / Num. of mol.: 1 / Mutation: K163Q-R164Q-K166Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RGA, GRS, RGA1, At2g01570, F2I9.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SLH3
#2: Protein Gibberellin receptor GID1A / AtCXE10 / Carboxylesterase 10 / GID1-like protein 1 / Protein GA INSENSITIVE DWARF 1A / AtGID1A


Mass: 39775.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GID1A, CXE10, GID1L1, At3g05120, T12H1.8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9MAA7, Hydrolases
#3: Protein F-box protein GID2 / Protein SLEEPY 1


Mass: 21069.963 Da / Num. of mol.: 1 / Mutation: E138K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GID2, SLY1, At4g24210, T22A6.40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9STX3
#4: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 21273.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39255
#5: Chemical ChemComp-GA3 / GIBBERELLIN A3 / (1S,2S,4aR,4bR,7S,9aS,10S,10aR)-2,7-dihydroxy-1-methyl-8-methylidene-13-oxo-1,2,4b,5,6,7,8,9,10,10a-decahydro-4a,1-(epo xymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid


Mass: 346.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22O6
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GA3-GID1A-RGA-SLY1-ASK1 Complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.21.2_5419 / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 556557 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047892
ELECTRON MICROSCOPYf_angle_d0.86910767
ELECTRON MICROSCOPYf_dihedral_angle_d6.3041210
ELECTRON MICROSCOPYf_chiral_restr0.0491248
ELECTRON MICROSCOPYf_plane_restr0.0071385

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