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- PDB-9o4j: Cryo-EM Structure of the Arabidopsis GA3-GID1A-RGA Complex -

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Basic information

Entry
Database: PDB / ID: 9o4j
TitleCryo-EM Structure of the Arabidopsis GA3-GID1A-RGA Complex
Components
  • DELLA protein RGA
  • Gibberellin receptor GID1A
KeywordsPLANT PROTEIN / RGA / GID1A / DELLA / Arabidopsis
Function / homology
Function and homology information


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 / negative 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 / negative regulation of gibberellic acid mediated signaling pathway / positive regulation of fertilization / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway / regulation of seed germination / response to far red light / Hydrolases / regulation of protein catabolic process / response to cold / promoter-specific chromatin binding / cellular response to hypoxia / hydrolase activity / transcription cis-regulatory region binding / DNA-binding transcription factor 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: 3.06 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.USA / Year: 2025
Title: Structural Insights into Proteolysis-Dependent and -Independent Suppression of the Master Regulator DELLA by Gibberellin Receptor
Authors: Dahal, P. / Wang, Y. / Hu, J. / Park, J. / Forker, K. / Zhang, Z. / Sharma, K. / Borgnia, M. / Sun, T.P. / Zhou, P.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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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)105,3763
Polymers105,0292
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: 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 / Comment: hormone*YM
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: RGA-GID1A-GA3 Complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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 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
9PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 398856 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046100
ELECTRON MICROSCOPYf_angle_d0.6728313
ELECTRON MICROSCOPYf_dihedral_angle_d6.123946
ELECTRON MICROSCOPYf_chiral_restr0.046939
ELECTRON MICROSCOPYf_plane_restr0.0041078

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