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- PDB-9luo: Cryo-EM structure of Arabidopsis thaliana RGA in complex with GID... -

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Basic information

Entry
Database: PDB / ID: 9luo
TitleCryo-EM structure of Arabidopsis thaliana RGA in complex with GID1A, SLY1, and ASK2 (focused map)
Components
  • DELLA protein RGA
  • F-box protein GID2
  • SKP1-like protein 1B
KeywordsHORMONE / Gibberellin / DELLA motif / GRAS domain / Plant growth
Function / homology
Function and homology information


regulation of gibberellic acid mediated signaling pathway / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / seed dormancy process / negative regulation of gibberellic acid mediated signaling pathway / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway ...regulation of gibberellic acid mediated signaling pathway / negative regulation of trichome patterning / negative regulation of developmental vegetative growth / negative regulation of leaf development / regulation of seed dormancy process / seed dormancy process / negative regulation of gibberellic acid mediated signaling pathway / meiotic cytokinesis / response to gibberellin / gibberellic acid mediated signaling pathway / regulation of seed germination / jasmonic acid mediated signaling pathway / seed germination / ethylene-activated signaling pathway / response to far red light / response to jasmonic acid / response to auxin / auxin-activated signaling pathway / embryo development ending in seed dormancy / SCF ubiquitin ligase complex / plastid / regulation of protein catabolic process / response to cold / chromosome segregation / promoter-specific chromatin binding / ubiquitin-dependent protein catabolic process / 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 / nucleus / cytosol
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-like domain superfamily ...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-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / 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
Similarity search - Domain/homology
SKP1-like protein 1B / DELLA protein RGA / F-box protein GID2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DELLA protein RGA
C: F-box protein GID2
D: SKP1-like protein 1B


Theoretical massNumber of molelcules
Total (without water)100,9913
Polymers100,9913
Non-polymers00
Water00
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: 64100.195 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 F-box protein GID2 / Protein SLEEPY 1


Mass: 17628.209 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: Q9STX3
#3: Protein SKP1-like protein 1B / SKP1-like 2 / UFO-binding protein 2


Mass: 19262.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1B, ASK2, UIP2, At5g42190, MJC20.30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FHW7
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: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer / Type: COMPLEX / Details: Partial model of RGA/GID1A/SLY/ASK2 heterotetramer / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.14 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
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65737 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.012585
ELECTRON MICROSCOPYf_angle_d1.0353481
ELECTRON MICROSCOPYf_dihedral_angle_d3.774330
ELECTRON MICROSCOPYf_chiral_restr0.035392
ELECTRON MICROSCOPYf_plane_restr0.005438

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