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- EMDB-70510: Cryo-EM Structure of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-70510
TitleCryo-EM Structure of the Arabidopsis GA3-GID1A-RGA-SLY1-ASK1 Complex (Alternative Conformation)
Map data
Sample
  • Complex: GA3-GID1A-RGA-SLY1-ASK1 Complex
    • Protein or peptide: DELLA protein RGA
    • Protein or peptide: Gibberellin receptor GID1A
    • Protein or peptide: F-box protein GID2
    • Protein or peptide: SKP1-like protein 1A
  • Ligand: GIBBERELLIN A3
KeywordsRGA / DELLA / GID1 / SLY1 / ASK1 / GA / PLANT PROTEIN
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
SKP1-like protein 1A / Gibberellin receptor GID1A / DELLA protein RGA / F-box protein GID2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 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
DepositionMay 6, 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_70510.png

Downloads & links

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Map

FileDownload / File: emd_70510.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8469 Å
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Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-22.030349999999999 - 52.420650000000002
Average (Standard dev.)-0.00059350283 (±1.0696713)
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_70510_msk_1.map
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Additional map: #1

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Half map: #1

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Half map: #2

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Sample components

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Entire : GA3-GID1A-RGA-SLY1-ASK1 Complex

EntireName: GA3-GID1A-RGA-SLY1-ASK1 Complex
Components
  • Complex: GA3-GID1A-RGA-SLY1-ASK1 Complex
    • Protein or peptide: DELLA protein RGA
    • Protein or peptide: Gibberellin receptor GID1A
    • Protein or peptide: F-box protein GID2
    • Protein or peptide: SKP1-like protein 1A
  • Ligand: GIBBERELLIN A3

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

SupramoleculeName: GA3-GID1A-RGA-SLY1-ASK1 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: DELLA protein RGA

MacromoleculeName: DELLA protein RGA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 65.253309 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRDHHQFQG RLSNHGTSSS SSSISKDKMM MVKKEEDGGG NMDDELLAVL GYKVRSSEMA EVALKLEQLE TMMSNVQEDG LSHLATDTV HYNPSELYSW LDNMLSELNP PPLPASSNGL DPVLPSPEIC GFPASDYDLK VIPGNAIYQF PAIDSSSSSN N QNQQLQSC ...String:
MKRDHHQFQG RLSNHGTSSS SSSISKDKMM MVKKEEDGGG NMDDELLAVL GYKVRSSEMA EVALKLEQLE TMMSNVQEDG LSHLATDTV HYNPSELYSW LDNMLSELNP PPLPASSNGL DPVLPSPEIC GFPASDYDLK VIPGNAIYQF PAIDSSSSSN N QNQQLQSC SSPDSMVTST STGTQIGGVI GTTVTTTTTT TTAAGESTRS VILVDSQENG VRLVHALMAC AEAIQQNNLT LA EALVKQI GCLAVSQAGA MRKVATYFAE ALARRIYRLS PPQNQIDHCL SDTLQMHFYE TCPYLKFAHF TANQAILEAF EGK KRVHVI DFSMNQGLQW PALMQALALR EGGPPTFRLT GIGPPAPDNS DHLHEVGCKL AQLAEAIHVE FEYRGFVANS LADL DASML ELRPSDTEAV AVNSVFELHK LLGRPGGIEK VLGVVKQIKP VIFTVVEQES NHNGPVFLDR FTESLHYYST LFDSL EGVP NSQDKVMSEV YLGKQICNLV ACEGPDRVER HETLSQWGNR FGSSGLAPAH LGSNAFKQAS MLLSVFNSGQ GYRVEE SNG CLMLGWHTRP LITTSAWKLS TAAYGGWSHP QFER

UniProtKB: DELLA protein RGA

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Macromolecule #2: Gibberellin receptor GID1A

MacromoleculeName: Gibberellin receptor GID1A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 39.775859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAASDEVNLI ESRTVVPLNT WVLISNFKVA YNILRRPDGT FNRHLAEYLD RKVTANANPV DGVFSFDVLI DRRINLLSRV YRPAYADQE QPPSILDLEK PVDGDIVPVI LFFHGGSFAH SSANSAIYDT LCRRLVGLCK CVVVSVNYRR APENPYPCAY D DGWIALNW ...String:
MAASDEVNLI ESRTVVPLNT WVLISNFKVA YNILRRPDGT FNRHLAEYLD RKVTANANPV DGVFSFDVLI DRRINLLSRV YRPAYADQE QPPSILDLEK PVDGDIVPVI LFFHGGSFAH SSANSAIYDT LCRRLVGLCK CVVVSVNYRR APENPYPCAY D DGWIALNW VNSRSWLKSK KDSKVHIFLA GDSSGGNIAH NVALRAGESG IDVLGNILLN PMFGGNERTE SEKSLDGKYF VT VRDRDWY WKAFLPEGED REHPACNPFS PRGKSLEGVS FPKSLVVVAG LDLIRDWQLA YAEGLKKAGQ EVKLMHLEKA TVG FYLLPN NNHFHNVMDE ISAFVNAECG GDYKDDDDK

UniProtKB: Gibberellin receptor GID1A

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Macromolecule #3: F-box protein GID2

MacromoleculeName: F-box protein GID2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 21.069963 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHHHHH ENLYFQSHMK RSTTDSDLAG DAHNETNKKM KSTEEEEIGF SNLDENLVYE VLKHVDAKTL AMSSCVSKIW HKTAQDERL WELICTRHWT NIGCGQNQLR SVVLALGGFR RLHSLYLWPL SKPNPRARFG KDELKLTLSL LSIRYYKKMS F TKRPLPES KGGWSHPQFE R

UniProtKB: F-box protein GID2

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Macromolecule #4: SKP1-like protein 1A

MacromoleculeName: SKP1-like protein 1A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 21.273586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHHHHH ENLYFQSHMS AKKIVLKSSD GESFEVEEAV ALESQTIAHM VEDDCVDNGV PLPNVTSKIL AKVIEYCKRH VEAAASKAE AVEGAATSDD DLKAWDADFM KIDQATLFEL ILAANYLNIK NLLDLTCQTV ADMIKGKTPE EIRTTFNIKN D FTPEEEEE VRRENQWAFE GGYKDDDDK

UniProtKB: SKP1-like protein 1A

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Macromolecule #5: GIBBERELLIN A3

MacromoleculeName: GIBBERELLIN A3 / type: ligand / ID: 5 / Number of copies: 1 / Formula: GA3
Molecular weightTheoretical: 346.374 Da
Chemical component information

ChemComp-GA3:
GIBBERELLIN A3

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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: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 556557
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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