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- EMDB-63401: Cryo-EM structure of Arabidopsis thaliana RGA in complex with GID... -

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Basic information

Entry
Database: EMDB / ID: EMD-63401
TitleCryo-EM structure of Arabidopsis thaliana RGA in complex with GID1A, SLY1, and ASK2 (composite map)
Map data
Sample
  • Complex: Heterotetramer of RGA, GID1A, SLY1, and ASK2
    • 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 1B
  • Ligand: GIBBERELLIN A3
KeywordsGibberellin / DELLA motif / GRAS domain / Plant growth / HORMONE
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 / regulation of seed germination / jasmonic acid mediated signaling pathway / seed germination / ethylene-activated signaling pathway / response to far red light / response to jasmonic acid / response to auxin / Hydrolases / auxin-activated signaling pathway / embryo development ending in seed dormancy / SCF ubiquitin ligase complex / plastid / regulation of protein catabolic process / response to cold / chromosome segregation / promoter-specific chromatin binding / 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 / 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 1B / Gibberellin receptor GID1A / DELLA protein RGA / F-box protein GID2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsIslam S / Park K / Kwon E / Kim DY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Plant / Year: 2025
Title: Structural insights into gibberellin-mediated DELLA protein degradation.
Authors: Soyaab Islam / Kunwoong Park / Jing Xia / Eunju Kwon / Dong Young Kim /
Abstract: Gibberellin promotes plant growth by downregulating DELLA proteins, which act as growth repressors. In the presence of gibberellin, the gibberellin receptor GID1 binds DELLA proteins, triggering ...Gibberellin promotes plant growth by downregulating DELLA proteins, which act as growth repressors. In the presence of gibberellin, the gibberellin receptor GID1 binds DELLA proteins, triggering their degradation through polyubiquitination by the SCF ubiquitin E3 ligase. Despite extensive studies, the molecular mechanisms by which DELLA proteins assemble with SCF to regulate plant growth remain poorly understood. Here, we present two cryo-electron microscopy structures of the Arabidopsis thaliana DELLA protein RGA in complex with GID1A and GID1A-SLY1-ASK2, respectively. Structural analyses revealed that RGA interacts with GID1A and SLY1 through nonoverlapping binding surfaces, stabilizing the proteins. This suggests that the SCF-RGA-GID1A complex assembles through a stepwise stabilization process induced by gibberellin. Furthermore, structural comparison with GRAS proteins indicates that RGA does not interact with IDD-family transcription factors when bound to SLY1, suggesting that DELLA protein binding to GID1/SLY1 and to transcription factors is mutually exclusive. These findings provide new insights into the gibberellin-mediated regulation of transcription factor activity by DELLA proteins.
History
DepositionFeb 9, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63401.png

Downloads & links

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Map

FileDownload / File: emd_63401.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.75 Å/pix.
x 400 pix.
= 298.04 Å		0.75 Å/pix.
x 400 pix.
= 298.04 Å		0.75 Å/pix.
x 400 pix.
= 298.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7451 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.369999999999999
Minimum - Maximum-41.652070000000002 - 55.076588000000001
Average (Standard dev.)0.00055715843 (±1.0397624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 298.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Heterotetramer of RGA, GID1A, SLY1, and ASK2

EntireName: Heterotetramer of RGA, GID1A, SLY1, and ASK2
Components
  • Complex: Heterotetramer of RGA, GID1A, SLY1, and ASK2
    • 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 1B
  • Ligand: GIBBERELLIN A3

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Supramolecule #1: Heterotetramer of RGA, GID1A, SLY1, and ASK2

SupramoleculeName: Heterotetramer of RGA, GID1A, SLY1, and ASK2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Heterotetramer of the DELLA protein RGA, gibberellin receptor GID1A, F-box protein SLY1, and SKP1-like protein ASK2
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 140 KDa

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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: 64.113125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSKRDHHQFQ GRLSNHGTSS SSSSISKDKM MMVKKEEDGG GNMDDELLAV LGYKVRSSEM AEVALKLEQL ETMMSNVQED GLSHLATDT VHYNPSELYS WLDNMLSELN PPPLPASSNG LDPVLPSPEI CGFPASDYDL KVIPGNAIYQ FPAIDSSSSS N NQNKRLKS ...String:
GSKRDHHQFQ GRLSNHGTSS SSSSISKDKM MMVKKEEDGG GNMDDELLAV LGYKVRSSEM AEVALKLEQL ETMMSNVQED GLSHLATDT VHYNPSELYS WLDNMLSELN PPPLPASSNG LDPVLPSPEI CGFPASDYDL KVIPGNAIYQ FPAIDSSSSS N NQNKRLKS CSSPDSMVTS TSTGTQIGGV IGTTVTTTTT TTTAAGESTR SVILVDSQEN GVRLVHALMA CAEAIQQNNL TL AEALVKQ IGCLAVSQAG AMRKVATYFA EALARRIYRL SPPQNQIDHC LSDTLQMHFY ETCPYLKFAH FTANQAILEA FEG KKRVHV IDFSMNQGLQ WPALMQALAL REGGPPTFRL TGIGPPAPDN SDHLHEVGCK LAQLAEAIHV EFEYRGFVAN SLAD LDASM LELRPSDTEA VAVNSVFELH KLLGRPGGIE KVLGVVKQIK PVIFTVVEQE SNHNGPVFLD RFTESLHYYS TLFDS LEGV PNSQDKVMSE VYLGKQICNL VACEGPDRVE RHETLSQWGN RFGSSGLAPA HLGSNAFKQA SMLLSVFNSG QGYRVE ESN GCLMLGWHTR PLITTSAWKL STAAY

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: 38.808922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMAASDEVN LIESRTVVPL NTWVLISNFK VAYNILRRPD GTFNRHLAEY LDRKVTANAN PVDGVFSFDV LIDRRINLLS RVYRPAYAD QEQPPSILDL EKPVDGDIVP VILFFHGGSF AHSSANSAIY DTLCRRLVGL CKCVVVSVNY RRAPENPYPC A YDDGWIAL ...String:
GSMAASDEVN LIESRTVVPL NTWVLISNFK VAYNILRRPD GTFNRHLAEY LDRKVTANAN PVDGVFSFDV LIDRRINLLS RVYRPAYAD QEQPPSILDL EKPVDGDIVP VILFFHGGSF AHSSANSAIY DTLCRRLVGL CKCVVVSVNY RRAPENPYPC A YDDGWIAL NWVNSRSWLK SKKDSKVHIF LAGDSSGGNI AHNVALRAGE SGIDVLGNIL LNPMFGGNER TESEKSLDGK YF VTVRDRD WYWKAFLPEG EDREHPACNP FSPRGKSLEG VSFPKSLVVV AGLDLIRDWQ LAYAEGLKKA GQEVKLMHLE KAT VGFYLL PNNNHFHNVM DEISAFVNAE C

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: 17.628209 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMKRSTTDS DLAGDAHNET NKKMKSTEEE EIGFSNLDEN LVYEVLKHVD AKTLAMSSCV SKIWHKTAQD ERLWELICTR HWTNIGCGQ NQLRSVVLAL GGFRRLHSLY LWPLSKPNPR ARFGKDELKL TLSLLSIRYY EKMSFTKRPL PESK

UniProtKB: F-box protein GID2

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Macromolecule #4: SKP1-like protein 1B

MacromoleculeName: SKP1-like protein 1B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 19.262406 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMSTVRKIT LKSSDGENFE IDEAVALESQ TIKHMIEDDC TDNGIPLPNV TSKILSKVIE YCKRHVEAAE KSETTADAAA ATTTTTVAS GSSDEDLKTW DSEFIKVDQG TLFDLILAAN YLNIKGLLDL TCQTVADMIK GKTPEEIRKT FNIKNDFTPE E EEEVRREN QWAFE

UniProtKB: SKP1-like protein 1B

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.7 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2183664
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65737
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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