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- PDB-9x5g: Cryo-EM structure of quinary complex GA3-MtGID1b-MtDELLA1-SLY1-ASK1 -

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Basic information

Entry
Database: PDB / ID: 9x5g
TitleCryo-EM structure of quinary complex GA3-MtGID1b-MtDELLA1-SLY1-ASK1
Components
  • DELLA protein 1
  • F-box protein GID2
  • Gibberellin receptor GID1c-like protein
  • SKP1-like protein 1A
KeywordsPLANT PROTEIN / GA
Function / homology
Function and homology information


response to symbiotic fungus / arbuscular mycorrhizal association / fruit morphogenesis / floral organ morphogenesis / positive regulation of gibberellic acid mediated signaling pathway / regulation of seed dormancy process / seed dormancy process / negative regulation of seed germination / gibberellin binding / negative regulation of gibberellic acid mediated signaling pathway ...response to symbiotic fungus / arbuscular mycorrhizal association / fruit morphogenesis / floral organ morphogenesis / positive regulation of gibberellic acid mediated signaling pathway / regulation of seed dormancy process / seed dormancy process / negative regulation of seed germination / gibberellin binding / negative regulation of gibberellic acid mediated signaling pathway / gibberellic acid mediated signaling pathway / phragmoplast / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / seed germination / male meiotic nuclear division / response to auxin / response to jasmonic acid / carboxylesterase activity / auxin-activated signaling pathway / negative regulation of DNA recombination / response to abscisic acid / cellular response to phosphate starvation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / chromosome segregation / microtubule cytoskeleton organization / spindle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / protein ubiquitination / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA-templated transcription / 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 / alpha/beta hydrolase fold / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
GIBBERELLIN A3 / DELLA protein 1 / Gibberellin receptor GID1c-like protein / SKP1-like protein 1A / F-box protein GID2
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsWan, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: Nat Commun / Year: 2026
Title: Structure-guided reprogramming of DELLA turnover for a sustainable Green Revolution in rice.
Authors: Chongyu Xue / Shuang Zhang / Lihao Wan / Zhihui Zhang / Chenchen Zhang / Huangqi Chen / Kai Peng / Yujie Wang / Jie Hu / Xiuhua Gao / Jiamu Du / Xiangdong Fu / Shutong Xu /
Abstract: The Green Revolution of the 1960s significantly boosted cereal yields but incurred substantial environmental costs due to overreliance on chemical fertilizer inputs; thus, future agricultural ...The Green Revolution of the 1960s significantly boosted cereal yields but incurred substantial environmental costs due to overreliance on chemical fertilizer inputs; thus, future agricultural sustainability demands improved nitrogen-use efficiency (NUE). The semi-dwarf Green Revolution varieties (GRVs) characterized by elevated DELLA protein accumulation introduce a fundamental trade-off, increasing lodging resistance and harvest index at the expense of diminished biomass and grain productivity per plant, and require high nitrogen fertilizer inputs to achieve maximum yield potential under high planting density. Here we show that gibberellin (GA)-bound GA-INSENSITIVE DWARF1 (GID1) induces multi-level conformational changes in DELLA protein, affecting its N-terminal DELLA and VHYN/DPT/S and C-terminal VVLV and SAW motifs, thereby facilitating recognition by the SKP1-CULLIN-F-box (SCF) ubiquitin ligase complex and subsequent proteasomal degradation. We also performed structure-guided engineering of the rice SLENDER RICE1 (SLR1)-GID1-GID2 complex and created a series of dwarf alleles exhibiting a continuous spectrum of plant heights in elite cultivars. Notably, the dominant alleles slr1 and slr1 achieved superior yield and enhanced NUE over conventional sd1-containing GRVs. Reprogramming DELLA turnover thus enables to break the long-standing trade-off between high yield and fertilizer dependency, offering a strategy toward a more sustainable and productive Green Revolution.
History
DepositionOct 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELLA protein 1
B: Gibberellin receptor GID1c-like protein
C: F-box protein GID2
D: SKP1-like protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7995
Polymers140,4524
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 1 / MtDELLA1


Mass: 65200.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: DELLA1, MTR_3g065980, MtrunA17_Chr3g0110971 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A396IUP1
#2: Protein Gibberellin receptor GID1c-like protein / Putative carboxylesterase


Mass: 39891.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11437344, MTR_7g093950, MtrunA17_Chr7g0259161 / Production host: Escherichia coli (E. coli) / References: UniProt: G7KWD5, carboxylesterase
#3: Protein F-box protein GID2 / Protein SLEEPY 1


Mass: 17484.148 Da / Num. of mol.: 1 / Mutation: E138K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GID2, SLY1, At4g24210, T22A6.40 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9STX3
#4: Protein SKP1-like protein 1A / SKP1-like 1 / UFO-binding protein 1


Mass: 17876.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SKP1A, ASK1, SKP1, UIP1, At1g75950, T4O12.17 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q39255
#5: 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
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: GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Medicago truncatula (barrel medic)3880
31Arabidopsis thaliana (thale cress)3702
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
31Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: METHANE

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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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121258 / Symmetry type: POINT
RefinementHighest resolution: 3.24 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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