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- EMDB-66586: Cryo-EM structure of Medicago truncatula GA3-GID1b-DELLA1 ternary... -

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Basic information

Entry
Database: EMDB / ID: EMD-66586
TitleCryo-EM structure of Medicago truncatula GA3-GID1b-DELLA1 ternary complex
Map data
Sample
  • Complex: Ternary complex of MtG-MtD-GA
    • Protein or peptide: DELLA protein 1
    • Protein or peptide: Gibberellin receptor GID1c-like protein
  • 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 / gibberellin binding / negative regulation of seed germination / negative regulation of gibberellic acid mediated signaling pathway / 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 / gibberellin binding / negative regulation of seed germination / negative regulation of gibberellic acid mediated signaling pathway / gibberellic acid mediated signaling pathway / carboxylesterase activity / response to abscisic acid / cellular response to phosphate starvation / sequence-specific DNA binding / 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 / nucleus / cytoplasm
Similarity search - Function
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. / : / Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. ...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. / : / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DELLA protein 1 / Gibberellin receptor GID1c-like protein
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsWan LH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: To Be Published
Title: MtG-MtD-GA
Authors: Wan LH
History
DepositionOct 13, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66586.png

Downloads & links

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Map

FileReleased
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: 3.0
Minimum - Maximum-0.11086331 - 15.765665
Average (Standard dev.)-0.028303746 (±0.4322973)
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_66586_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_66586_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of MtG-MtD-GA

EntireName: Ternary complex of MtG-MtD-GA
Components
  • Complex: Ternary complex of MtG-MtD-GA
    • Protein or peptide: DELLA protein 1
    • Protein or peptide: Gibberellin receptor GID1c-like protein
  • Ligand: GIBBERELLIN A3

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Supramolecule #1: Ternary complex of MtG-MtD-GA

SupramoleculeName: Ternary complex of MtG-MtD-GA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Medicago truncatula (barrel medic)

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Macromolecule #1: Gibberellin receptor GID1c-like protein

MacromoleculeName: Gibberellin receptor GID1c-like protein / type: protein_or_peptide / ID: 1 / 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 #2: DELLA protein 1

MacromoleculeName: DELLA protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Medicago truncatula (barrel medic)
Molecular weightTheoretical: 65.072648 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 EENTAASSMK TWSEPESEPA VVMSPPPAVE NTRPVVLVDT QETGVRLVHT LMACAEAIQQ KNLKLAEALV KH ISLLASL QTGAMRKVAS YFAQALARRI YGNPEETIDS SFSEILHMHF YESSPYLKFA HFTANQAILE AFAGAGRVHV IDF GLKQGM QWPALMQALA LRPGGPPTFR LTGIGPPQAD NTDALQQVGW KLAQLAQTIG VQFEFRGFVS 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 #3: GIBBERELLIN A3

MacromoleculeName: GIBBERELLIN A3 / type: ligand / ID: 3 / 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: 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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 55910
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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