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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 / gibberellin binding / negative regulation of seed germination / 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 / gibberellin binding / negative regulation of seed germination / 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 / response to auxin / response to jasmonic acid / carboxylesterase activity / male meiotic nuclear division / 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 / sequence-specific DNA binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / 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 / 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: To Be Published
Title: MtG-MtD-GA
Authors: Wan, L.H.
History
DepositionOct 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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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