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- EMDB-66587: Cryo-EM structure of quinary complex GA3-MtGID1b-MtDELLA1-SLY1-ASK1 -

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Basic information

Entry
Database: EMDB / ID: EMD-66587
TitleCryo-EM structure of quinary complex GA3-MtGID1b-MtDELLA1-SLY1-ASK1
Map data
Sample
  • Complex: GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex
    • Protein or peptide: DELLA protein 1
    • Protein or peptide: Gibberellin receptor GID1c-like protein
    • Protein or peptide: F-box protein GID2
    • Protein or peptide: SKP1-like protein 1A
  • Ligand: GIBBERELLIN A3
KeywordsGA / PLANT PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsWan LH
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66587.png

Downloads & links

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Map

FileDownload / File: emd_66587.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.10336359 - 15.679088
Average (Standard dev.)-0.011933361 (±0.46817303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66587_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66587_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex

EntireName: GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex
Components
  • Complex: GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex
    • Protein or peptide: DELLA protein 1
    • Protein or peptide: Gibberellin receptor GID1c-like protein
    • Protein or peptide: F-box protein GID2
    • Protein or peptide: SKP1-like protein 1A
  • Ligand: GIBBERELLIN A3

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Supramolecule #1: GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex

SupramoleculeName: GA3-MtGID1b-MtDELLA1-SLY1E138K-ASK1 pentameric complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Medicago truncatula (barrel medic)

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Macromolecule #1: DELLA protein 1

MacromoleculeName: DELLA protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Medicago truncatula (barrel medic)
Molecular weightTheoretical: 65.20093 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKREHQESFG GGVISNNNKT NTNHLNSSKN INFGECSSMQ NTNTKQNMWR EEKETNGGGM DELLAALGYK VRSSDMADVA QKLEQLEMV MGSAQEEGIN HLSSDTVHYD PTDLYSWVQT MLTELNPDSS QINDPLASLG SSEILNNTFN DDSEYDLSAI P GMAAYPPQ ...String:
MKREHQESFG GGVISNNNKT NTNHLNSSKN INFGECSSMQ NTNTKQNMWR EEKETNGGGM DELLAALGYK VRSSDMADVA QKLEQLEMV MGSAQEEGIN HLSSDTVHYD PTDLYSWVQT MLTELNPDSS QINDPLASLG SSEILNNTFN DDSEYDLSAI P GMAAYPPQ EENTAAKRMK TWSEPESEPA VVMSPPPAVE NTRPVVLVDT QETGVRLVHT LMACAEAIQQ KNLKLAEALV KH ISLLASL QTGAMRKVAS YFAQALARRI YGNPEETIDS SFSEILHMHF YESSPYLKFA HFTANQAILE AFAGAGRVHV IDF GLKQGM QWPALMQALA LRPGGPPTFR LTGIGPPQAD NTDALQQVGW KLAQLAQTIG VQFEFRGFVC NSIADLDPNM LEIR PGEAV AVNSVFELHT MLARPGSVEK VLNTVKKINP KIVTIVEQEA NHNGPVFVDR FTEALHYYSS LFDSLEGSNS SSNNS NSNS TGLGSPSQDL LMSEIYLGKQ ICNVVAYEGV DRVERHETLT QWRSRMGSAG FEPVHLGSNA FKQASTLLAL FAGGDG YRV EENNGCLMLG WHTRSLIATS AWKLPQNESK

UniProtKB: DELLA protein 1

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Macromolecule #2: Gibberellin receptor GID1c-like protein

MacromoleculeName: Gibberellin receptor GID1c-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: carboxylesterase
Source (natural)Organism: Medicago truncatula (barrel medic)
Molecular weightTheoretical: 39.891191 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTGTNEVNLS ESRSVVPLNT YVLISNFKLA YNLLRRADGT FNRDLAEFLD RKVPANAIPV DGVFSFDHIE RNTGLFNRVY LPSSSENES QWGVKDLEKP LSTTEIVPVI VFFHGGSFSH SSANSAIYDT FCRRLVSVCK AAVVSVNYRR SPEYRFPCAY E DGWNALKW ...String:
MTGTNEVNLS ESRSVVPLNT YVLISNFKLA YNLLRRADGT FNRDLAEFLD RKVPANAIPV DGVFSFDHIE RNTGLFNRVY LPSSSENES QWGVKDLEKP LSTTEIVPVI VFFHGGSFSH SSANSAIYDT FCRRLVSVCK AAVVSVNYRR SPEYRFPCAY E DGWNALKW VKSRKWLQSG KEKKVYVYMA GDSSGGNIVH HVAVKACEEK AEGIEVLGNI LLHPLFGGEK RTDSEMRLDG KY FVRLQDR DWYWRAFLPE GEDRDHPACN PFGPKGEKNI KGLDKFPKSL VCVAGLDLLQ DWQLAYVDGL RNFGQDVKLL YLK EATIGF YFLPNNDHFY CLMEEIKNFV NPNC

UniProtKB: Gibberellin receptor GID1c-like protein

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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: 17.484148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MKRSTTDSDL AGDAHNETNK KMKSTEEEEI GFSNLDENLV YEVLKHVDAK TLAMSSCVSK IWHKTAQDER LWELICTRHW TNIGCGQNQ LRSVVLALGG FRRLHSLYLW PLSKPNPRAR FGKDELKLTL SLLSIRYYKK MSFTKRPLPE SK

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: 17.876043 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSAKKIVLKS SDGESFEVEE AVALESQTIA HMVEDDCVDN GVPLPNVTSK ILAKVIEYCK RHVEAAASKA EAVEGAATSD DDLKAWDAD FMKIDQATLF ELILAANYLN IKNLLDLTCQ TVADMIKGKT PEEIRTTFNI KNDFTPEEEE EVRRENQWAF E

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 / hormone*YM

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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: 8
VitrificationCryogen name: METHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121258
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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