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- PDB-9lum: Cryo-EM structure of Arabidopsis thaliana RGA in complex with GID1A -

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Basic information

Entry
Database: PDB / ID: 9lum
TitleCryo-EM structure of Arabidopsis thaliana RGA in complex with GID1A
Components
  • DELLA protein RGA
  • Gibberellin receptor GID1A
KeywordsHORMONE / Gibberellin / DELLA motif / GRAS domain / Plant growth
Function / homology
Function and homology information


fruit morphogenesis / gibberellin mediated signaling pathway / raffinose family oligosaccharide biosynthetic process / floral organ morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / positive regulation of gibberellic acid mediated signaling pathway / gibberellin binding ...fruit morphogenesis / gibberellin mediated signaling pathway / raffinose family oligosaccharide biosynthetic process / floral organ morphogenesis / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / positive regulation of gibberellic acid mediated signaling pathway / gibberellin binding / negative regulation of gibberellic acid mediated signaling pathway / positive regulation of fertilization / salicylic acid mediated signaling pathway / meiotic cytokinesis / negative regulation of seed germination / response to gibberellin / gibberellic acid mediated signaling pathway / response to ethylene / regulation of seed germination / jasmonic acid mediated signaling pathway / response to far red light / hyperosmotic salinity response / Hydrolases / response to abscisic acid / regulation of reactive oxygen species metabolic process / regulation of protein catabolic process / response to cold / promoter-specific chromatin binding / cellular response to hypoxia / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / hydrolase activity / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
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. / : / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. ...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. / : / 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 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
GIBBERELLIN A3 / Gibberellin receptor GID1A / DELLA protein RGA
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsIslam, S. / Park, K. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Plant / Year: 2025
Title: Structural insights into gibberellin-mediated DELLA protein degradation.
Authors: Soyaab Islam / Kunwoong Park / Jing Xia / Eunju Kwon / Dong Young Kim /
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 ...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 ubiquitin E3 ligase. Despite extensive studies, the molecular mechanisms by which DELLA proteins assemble with SCF 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-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.
History
DepositionFeb 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.title / _em_admin.last_update
Revision 1.2Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DELLA protein RGA
B: Gibberellin receptor GID1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2683
Polymers102,9222
Non-polymers3461
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 64113.125 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: Q9SLH3
#2: Protein Gibberellin receptor GID1A / AtCXE10 / Carboxylesterase 10 / GID1-like protein 1 / Protein GA INSENSITIVE DWARF 1A / AtGID1A


Mass: 38808.922 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 BL21(DE3) (bacteria) / References: UniProt: Q9MAA7, Hydrolases
#3: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Heterodimer of RGA and GID1A/GA3 / Type: COMPLEX
Details: Heterodimer of the DELLA protein RGA and gibberellin receptor GID1A in complex with gibberellin A3
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.103 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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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 defocus max: 2700 nm / Nominal defocus min: 600 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
2PHENIX1.20.1_4487:model refinement
5cryoSPARC4.4.0CTF correction
13cryoSPARC4.4.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2804928
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251864 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.016214
ELECTRON MICROSCOPYf_angle_d1.1388443
ELECTRON MICROSCOPYf_dihedral_angle_d4.207836
ELECTRON MICROSCOPYf_chiral_restr0.04939
ELECTRON MICROSCOPYf_plane_restr0.0081094

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