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- EMDB-70106: Cryo-EM Local Refinement Map (GA3-GID1A-RGA) of the Arabidopsis G... -

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Basic information

Entry
Database: EMDB / ID: EMD-70106
TitleCryo-EM Local Refinement Map (GA3-GID1A-RGA) of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Complex
Map dataLocal Refinement Map
Sample
  • Complex: RGA-GID1A-GA3-SLY1-ASK1
KeywordsRGA / GID1A / SLY1 / ASK1 / SKP1 / SCF / PLANT PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsDahal P / Sharma K / Borgnia M / Zhou P
Funding support United States, 1 items
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
DepositionApr 8, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70106.png

Downloads & links

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Map

FileDownload / File: emd_70106.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal Refinement Map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.008 Å		0.85 Å/pix.
x 320 pix.
= 271.008 Å		0.85 Å/pix.
x 320 pix.
= 271.008 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8469 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0899497 - 0.19343105
Average (Standard dev.)-0.00019686765 (±0.0038252503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70106_msk_1.map
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Additional map: #1

Fileemd_70106_additional_1.map
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Half map: #2

Fileemd_70106_half_map_1.map
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Half map: #1

Fileemd_70106_half_map_2.map
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Sample components

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Entire : RGA-GID1A-GA3-SLY1-ASK1

EntireName: RGA-GID1A-GA3-SLY1-ASK1
Components
  • Complex: RGA-GID1A-GA3-SLY1-ASK1

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Supramolecule #1: RGA-GID1A-GA3-SLY1-ASK1

SupramoleculeName: RGA-GID1A-GA3-SLY1-ASK1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 620689
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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